kitten-only_genus-level_thesis-graphs.R

#### All dataset, graphics for thesis
#genus level

### install packages
#BiocManager::install("limma")
#BiocManager::install("ANCOMBC")
#BiocManager::install("Maaslin2")
#BiocManager::install("biomformat")
#install.packages("remotes")
#remotes::install_github("vmikk/metagMisc")
#BiocManager::install("readxl")
#BiocManager::install("mixOmics")
#BiocManager::install("microbiome")

## Load librarys
library(limma)
library(ANCOMBC)

## Warning in check_dep_version(): ABI version mismatch: 
## lme4 was built with Matrix ABI version 1
## Current Matrix ABI version is 0
## Please re-install lme4 from source or restore original 'Matrix' package

library(Maaslin2)
library(phyloseq)
library(tidyverse)

## Warning: package 'ggplot2' was built under R version 4.3.3

## Warning: package 'tidyr' was built under R version 4.3.3

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.4     ✔ readr     2.1.5
## ✔ forcats   1.0.0     ✔ stringr   1.5.1
## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
## ✔ purrr     1.0.2     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

library(biomformat)
library(metagMisc)

## 
## Attaching package: 'metagMisc'
## 
## The following object is masked from 'package:purrr':
## 
##     some

library(readxl)
library(mixOmics)

## Loading required package: MASS
## 
## Attaching package: 'MASS'
## 
## The following object is masked from 'package:dplyr':
## 
##     select
## 
## Loading required package: lattice
## 
## Loaded mixOmics 6.26.0
## Thank you for using mixOmics!
## Tutorials: http://mixomics.org
## Bookdown vignette: https://mixomicsteam.github.io/Bookdown
## Questions, issues: Follow the prompts at http://mixomics.org/contact-us
## Cite us:  citation('mixOmics')
## 
## 
## Attaching package: 'mixOmics'
## 
## The following object is masked from 'package:purrr':
## 
##     map

library(vegan)

## Warning: package 'vegan' was built under R version 4.3.3

## Loading required package: permute
## This is vegan 2.6-4

library(RColorBrewer)
library(microbiome)

## 
## microbiome R package (microbiome.github.com)
##     
## 
## 
##  Copyright (C) 2011-2022 Leo Lahti, 
##     Sudarshan Shetty et al. <microbiome.github.io>
## 
## 
## Attaching package: 'microbiome'
## 
## The following object is masked from 'package:vegan':
## 
##     diversity
## 
## The following object is masked from 'package:metagMisc':
## 
##     prevalence
## 
## The following object is masked from 'package:ggplot2':
## 
##     alpha
## 
## The following object is masked from 'package:base':
## 
##     transform

#devtools::install_github("jbisanz/qiime2R")
library(devtools)

## Loading required package: usethis

## Warning: package 'usethis' was built under R version 4.3.3

## 
## Attaching package: 'devtools'
## 
## The following object is masked from 'package:permute':
## 
##     check

library(qiime2R)
library(tidyverse)

#if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")}
#devtools::install_github("jbisanz/qiime2R")
library(devtools)
library(qiime2R)
library(tidyverse)

library(phyloseq)
#install.packages(c("devtools", "RcppEigen", "RcppParallel", "Rtsne", "ggforce", "units"))
#devtools::install_github('schuyler-smith/phylosmith')
library(phylosmith)

setwd("C:/Users/rowen1/OneDrive - Massey University/CA Reasearch/Masters Project/Thesis data/Kitten D+ datasets_FINAL_17092024")


# Kitten only
Ktaxonomy<-read_qza("KittenOnly_17092024/taxonomy.qza")
KSVs<-read_qza("KittenOnly_17092024/table-12.qza")
Kmetadata <- read_delim("KittenOnly_17092024/kittenOnlyMeta_FINAL.txt") 

## Rows: 49 Columns: 31
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (21): sampleid, litter, sample, sample_type, timing, litter_type, kitten...
## dbl (10): litter_number, age_weaned_wk, age_weaned_day, week, age_wk, age_da...
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Ktree <- read_qza("KittenOnly_17092024/rooted-tree.qza")
Kshannon <-read_qza("KittenOnly_17092024/core-metrics-results/shannon_vector.qza")


Kphyseq<-qza_to_phyloseq(
  taxonomy = "KittenOnly_17092024/taxonomy.qza",
  features = "KittenOnly_17092024/table-12.qza",
  tree = "KittenOnly_17092024/rooted-tree.qza",
  metadata = "KittenOnly_17092024/kittenOnlyMeta_FINAL.txt")

Kphyseq

## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 9337 taxa and 49 samples ]
## sample_data() Sample Data:       [ 49 samples by 30 sample variables ]
## tax_table()   Taxonomy Table:    [ 9337 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 9337 tips and 9280 internal nodes ]

####----------------------------------------------------------------------------------------------------------

## Normalise
### https://yiluheihei.github.io/microbiomeMarker/reference/normalize-methods.html 

#install.packages("microbial")
library(microbial)

## 
## Attaching package: 'microbial'
## 
## The following object is masked from 'package:microbiome':
## 
##     richness
## 
## The following objects are masked from 'package:phyloseq':
## 
##     otu_table, phy_tree, psmelt, sample_data, subset_samples,
##     subset_taxa, tax_table

Kphyseq_norm <- normalize(Kphyseq, method = "CLR")

#Prune taxa 
# Agglomerate taxa at phylum level
Kphyseq_norm_genus <- tax_glom(Kphyseq_norm, taxrank = "Genus")

# Top N taxa
N <- 10
top <- names(sort(taxa_sums(Kphyseq_norm_genus), decreasing = TRUE))[1:N]

# Calculate relative abundance
Kphyseq_norm_genus_prop <- transform_sample_counts(Kphyseq_norm_genus, function(x) x / sum(x) )

# Subset object to top N taxa
Kphyseq_norm_genus_prop_top <- prune_taxa(top, Kphyseq_norm_genus_prop)

Kphyseq_norm_genus_prop_top

## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 10 taxa and 49 samples ]
## sample_data() Sample Data:       [ 49 samples by 30 sample variables ]
## tax_table()   Taxonomy Table:    [ 10 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 10 tips and 9 internal nodes ]

Kphyseq_norm_genus_prop

## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 392 taxa and 49 samples ]
## sample_data() Sample Data:       [ 49 samples by 30 sample variables ]
## tax_table()   Taxonomy Table:    [ 392 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 392 tips and 391 internal nodes ]

#### Sample type combined graphics

##Alpha diversity
##https://www.nicholas-ollberding.com/post/introduction-to-phyloseq/
#pdf("Kphyseq_sample type analysis_kitten only.pdf",height=6,width=8,pointsize=15)
head(estimate_richness(Kphyseq))

##     Observed    Chao1  se.chao1      ACE    se.ACE  Shannon   Simpson
## X10      467 467.0185 0.1416587 467.5622 10.798213 4.084574 0.9702991
## X11      396 396.0476 0.2288603 397.0564  9.942537 3.770247 0.9574684
## X12      413 413.0200 0.1476714 413.5525 10.151408 3.726533 0.9541814
## X13      665 665.0312 0.1824670 665.8932 12.862596 3.763168 0.9420338
## X14      398 398.0164 0.1326892 398.6201  9.968236 3.715440 0.9574987
## X23      548 548.0508 0.2372249 548.8994 11.700436 3.958817 0.9366669
##     InvSimpson   Fisher
## X10   33.66896 63.80074
## X11   23.51194 54.90173
## X12   21.82518 56.75878
## X13   17.25142 95.84068
## X14   23.52872 55.82140
## X23   15.78952 81.39638

(A <- plot_richness(Kphyseq, x = "sample_type", color = "sample_type", measures = c("Observed", "Shannon", "Chao1")))

A + labs(x = "", y = "Alpha Diversity Measure\n") + 
  geom_boxplot()

###########################################################################################
#### Code to get to PCA
###############  Now remove low abundance taxa: 
###############


#tax_level <- "genus"   ## analyse at genus level. Not needed with newer version of R.
Kphyseq.tax.level <- tax_glom(Kphyseq, taxrank = "Genus")   # Make new phyloseq object at tax level
#??tax_glom

dim(Kphyseq.tax.level@otu_table)  # size of table

## [1] 392  49

Kphyseq.tax.level@tax_table   #  new tax hierarchy - 431 at Genus level 

## Taxonomy Table:     [392 taxa by 7 taxonomic ranks]:
##                                  Kingdom    Phylum            
## 738f9b43067c64d7dd19a58e16776ca1 "Archaea"  "Euryarchaeota"   
## bf3ea7575ee681f6cc071fc10a9b0c9e "Archaea"  "Euryarchaeota"   
## 81ca8fa4a795e9929b18c343fa7e5d6d "Archaea"  "Euryarchaeota"   
## fce80713066a40d6d40c78a2bfc701f0 "Bacteria" "Fusobacteria"    
## da2d307acbc750e709821f37106a97ee "Bacteria" "Fusobacteria"    
## ec4dafd949562cb1c67abf1edb908e45 "Bacteria" "Fusobacteria"    
## 937486517cc80db8a7247c8d9cedcb6c "Bacteria" "Fusobacteria"    
## 2960c4868268ab63fffd54d389e709f4 "Bacteria" "Tenericutes"     
## b1cc0afab8aabe335f3d2183a8f862a8 "Bacteria" "[Thermi]"        
## d812033144facb838340db156bc7cddb "Bacteria" "[Thermi]"        
## a8d5e516d55e0f840a901a1754faf215 "Bacteria" "[Thermi]"        
## b3f7ce9240052a0925ec9e675b5c5801 "Bacteria" "[Thermi]"        
## dd2c236c7e7f2b0eca6a81e2ac82e5e9 "Bacteria" "[Thermi]"        
## f572830d714e07d0b571ccb4029c577b "Bacteria" "[Thermi]"        
## 12c129f217c4ceeb3f4e6992749ee828 "Bacteria" "Armatimonadetes" 
## 1ef109986a98fbad2514a0bdde298328 "Bacteria" "Bacteroidetes"   
## 550a6c75a980e53ebe63fb821d692cf3 "Bacteria" "Bacteroidetes"   
## 08790daac50cd048ed5839225585e108 "Bacteria" "Bacteroidetes"   
## 9cbea8ff52e16e14d63f27d5f6f9ee70 "Bacteria" "Bacteroidetes"   
## 38876d2e7234ac8c535d914e1b89c7f2 "Bacteria" "Bacteroidetes"   
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## 2c234c87c5882dd4f414aec10fa936c2 "Bacteria" "Firmicutes"      
## 0f1caf1bbdbe6b2ca659622ee70d0b63 "Bacteria" "Firmicutes"      
## e5c43f196cbe5ab66faa3c4f467a0886 "Bacteria" "Firmicutes"      
## 6b085c4046ac5ebe8ef6ac62d791bea5 "Bacteria" "Firmicutes"      
## c00d929bb5c22936acc74570e3b5bdf6 "Bacteria" "Firmicutes"      
## 1d05ba400871e661d4b6f5d5221ceaa0 "Bacteria" "Firmicutes"      
## 4580887b2b9919823d69f37282c7eb68 "Bacteria" "Firmicutes"      
## 2e398b8d21dc0766b2cf014de5f215f9 "Bacteria" "Firmicutes"      
## babb2ebb5ca6d5b569dbcd2b4b628198 "Bacteria" "Firmicutes"      
## bf2c7a63827bc0b6e73780bd35ef1b24 "Bacteria" "Firmicutes"      
## a5d29f17bd1a64838e0d611fbcdd1ff6 "Bacteria" "Firmicutes"      
## 3c7e37f4083b0b16aa9124dad86730c7 "Bacteria" "Firmicutes"      
## 045316716e32037c41e0b163bf4d7f21 "Bacteria" "Tenericutes"     
## d8f53497fb4a7d7ece0196fb9f0a6ab4 "Bacteria" "Proteobacteria"  
## 5cfcdb0adca683f26388b734166fa45b "Bacteria" "Proteobacteria"  
## d372fbcdc973cce384300297bee0478f "Bacteria" "Proteobacteria"  
## ae33131a40a790d5a6e096dfe63a89d8 "Bacteria" "Proteobacteria"  
## 187e9220f0344b3c3fa9269ef230fc90 "Bacteria" "Proteobacteria"  
## 672ee70217e3b5a9235307922a02c7f8 "Bacteria" "Proteobacteria"  
## 5e056cc118579d9d7c95fe778b8ea768 "Bacteria" "Proteobacteria"  
## 9b487aae59ee8631f146add439f853d2 "Bacteria" "Proteobacteria"  
## 1ae19e5736f0e1386f60a9f7c5d78fde "Bacteria" "Proteobacteria"  
## 0ab39039498ea9d85c86e8123448534b "Bacteria" "Proteobacteria"  
## 653b92284cc9d8af71788389322f0edd "Bacteria" "Proteobacteria"  
## e21fc8d6fb72d301fc9c60d5767cce74 "Bacteria" "Proteobacteria"  
## e8707202237b30ae28569d165c85bf19 "Bacteria" "Proteobacteria"  
## f889b0623697ffab382195032c9ad941 "Bacteria" "Proteobacteria"  
## 305ad58751bd60cdfb4c103af7c099f4 "Bacteria" "Proteobacteria"  
## 045260d3560e65d1ed7fc1184847d2ab "Bacteria" "Proteobacteria"  
## f31d96a0dc85b58019e54c41729a5705 "Bacteria" "Proteobacteria"  
## 801ac076ebb43dd3c879924efd470f18 "Bacteria" "Proteobacteria"  
## 7c71dd18459d57c725a3ad9ec173d5db "Bacteria" "Proteobacteria"  
## 32391b052e2eb6e82b519a21b917701a "Bacteria" "Proteobacteria"  
## 90023f83f20dc4626e11297485a2a460 "Bacteria" "Proteobacteria"  
## f79e941eee754904cdc3e35d0786a2bd "Bacteria" "Proteobacteria"  
## 892d322ffc17d6b4821998ef14e94580 "Bacteria" "Proteobacteria"  
## 9b44baa49a601fb4b6c50c312c901778 "Bacteria" "Proteobacteria"  
## cbb4db0a376d0da10f3409b324e572b3 "Bacteria" "Proteobacteria"  
## 2926f7065c61a289014e2ef920198e41 "Bacteria" "Proteobacteria"  
## b90f313249467f3247b2e178108f56c4 "Bacteria" "Proteobacteria"  
## 9fb82f32eb82975222f78b04260eaa3a "Bacteria" "Proteobacteria"  
## 23ccd8e52a41d7ca1cd3f7d18bb747b7 "Bacteria" "Proteobacteria"  
## 2de364e6eaebebbbb28cca6b2ee5f322 "Bacteria" "Proteobacteria"  
## 100dda46eb1c9633ba33d459cad7b6d3 "Bacteria" "Proteobacteria"  
## 2027d883259942129f4653bb8773ccbb "Bacteria" "Proteobacteria"  
## adce59f1751d627ceab8dd97f4d04c6f "Bacteria" "Proteobacteria"  
## 4be80be705379fe624bf4f236868c161 "Bacteria" "Proteobacteria"  
## 0c8e4b53a95f728aad2fb84bbd346f97 "Bacteria" "Proteobacteria"  
## efbb12b0a03e0073ea00bee12f98b36e "Bacteria" "Proteobacteria"  
## 1d38cdf4c8a50b1ea96f2156356de988 "Bacteria" "Proteobacteria"  
## 19a6bf2bac2f1eda36feda7b342d2fb5 "Bacteria" "Proteobacteria"  
## 27105df2940b9391e03c2d80d7f8b4f5 "Bacteria" "Proteobacteria"  
## 939aeb8878169f64a49619412a2f63b0 "Bacteria" "Proteobacteria"  
## e0e1b66edfc9669ea0d9a6a802bf2788 "Bacteria" "Proteobacteria"  
## d89d2a592c1aca630b867e7ccb9e42a6 "Bacteria" "Proteobacteria"  
## 5cf7e8ff515a6a5f6104637fd70423c1 "Bacteria" "Proteobacteria"  
## 69a578040fb5a9fff8bc026b7909ba83 "Bacteria" "Proteobacteria"  
## fbf60a3c4454aa9de8e64561fccc5345 "Bacteria" "Proteobacteria"  
## a1d7db2eb229495c2c82b6983acf7e43 "Bacteria" "Proteobacteria"  
## 17fad4dc8312a2057293bfc76005b8de "Bacteria" "Proteobacteria"  
## 73dc5d7d8e076fd5a6aeddf13f9ef785 "Bacteria" "Proteobacteria"  
## 133220fc9566f8823ba6361d973f7e56 "Bacteria" "Proteobacteria"  
## 11a0aa4ba2b9f7349d89e260f7091c23 "Bacteria" "Proteobacteria"  
## 8a8122d28d426c268bc33a6036ee1201 "Bacteria" "Proteobacteria"  
## 56f83521d186287a1334d08d18f63158 "Bacteria" "Proteobacteria"  
## 8987bf7650d847a8389432b1b97b9076 "Bacteria" "Proteobacteria"  
## c99ed97ec81f07d7a5bf5e6d39644e78 "Bacteria" "Proteobacteria"  
## 79d01cf1a57f4ae9b2100a92fc8ccdba "Bacteria" "Proteobacteria"  
## 49d4b7fc67aed6a6c15b45b14ec2d0bd "Bacteria" "Proteobacteria"  
## 787102493891f91105723053cb7fa472 "Bacteria" "Proteobacteria"  
## 83cfc0b49f561f34323bf84f88479fb0 "Bacteria" "Proteobacteria"  
## ed4ce9dc264e70619df3ec76f6551fd6 "Bacteria" "Proteobacteria"  
## ac967d4c0addb4554c76a32d34fd6c95 "Bacteria" "Proteobacteria"  
## 438f1f8281a645f62d60881fd6b0fa57 "Bacteria" "Proteobacteria"  
## 7fc26bb3199fb45b03be3a64086369fc "Bacteria" "Proteobacteria"  
## 69c2a11ae089bcd6b89a7e0e820348a0 "Bacteria" "Proteobacteria"  
## a1a04d3b99a0830ff52c65019cdbf0ae "Bacteria" "Proteobacteria"  
## cb8975338b82a1cde52ea64147755a73 "Bacteria" "Proteobacteria"  
## cbcf57af593627cc223bc600b5fb8318 "Bacteria" "Proteobacteria"  
## dad64d6402e87f2685829f369810b4da "Bacteria" "Proteobacteria"  
## 1d4ba0b34502c3002f4e746231e00d5f "Bacteria" "Proteobacteria"  
## a8f07c39cca53fb138e8007eb22aa6a1 "Bacteria" "Proteobacteria"  
## 94ea0cf0f0fc7c8f21b14c876a6531e5 "Bacteria" "Proteobacteria"  
## d689bc688fc4d75a7bb96dae07c80129 "Bacteria" "Proteobacteria"  
## 085877117ce16b29716cb7211f5bf8e0 "Bacteria" "Proteobacteria"  
## 6e8ddec699ec02deed4236f0af079318 "Bacteria" "Proteobacteria"  
## dc5b0a8becafb8ce2ca3326fc498464b "Bacteria" "Proteobacteria"  
## 1d4f2df9b6265023cd7a291fd570f21d "Bacteria" "Proteobacteria"  
## 9b740e8e047c98bb45cd4dc582c1a7f9 "Bacteria" "Proteobacteria"  
## b8a850e18c6624af91cd225fbdefa983 "Bacteria" "Proteobacteria"  
## e648c38b1b9e6300c7919c49b32f2d6f "Bacteria" "Proteobacteria"  
## c1889e2c77161500555ea720c5850b61 "Bacteria" "Proteobacteria"  
## 9b6c084f78f830b31a28de8180814ae8 "Bacteria" "Proteobacteria"  
## 88242931b35810f68ef8dd396bb1d337 "Bacteria" "Proteobacteria"  
## 3e155bea0907cecaf362cac4e87deb3d "Bacteria" "Proteobacteria"  
## 5e55605eb003f98493386574e7670725 "Bacteria" "Proteobacteria"  
## 14f6c55698300e24e20f0af01fc1362a "Bacteria" "Proteobacteria"  
## d59a2064644c08d1dadbbce20f19f527 "Bacteria" "Proteobacteria"  
## 20e66d19c6e48da230746eb8df4fbee9 "Bacteria" "Proteobacteria"  
## db18ee1beaf8b0931f49185b7e87bb50 "Bacteria" "Proteobacteria"  
## 5bddc3e2dd40027af0348e3e496b5ede "Bacteria" "Proteobacteria"  
## 98c0af570beeb456ca1529e4b7539b6c "Bacteria" "Proteobacteria"  
## 325c677d23378529799356c93bdbf138 "Bacteria" "Proteobacteria"  
## 184c1055f8871453d4cfb2e063826c79 "Bacteria" "Proteobacteria"  
## 8454ff06fc777ee1792f0a92c0a2a3db "Bacteria" "Proteobacteria"  
## 139b3a842bac5a67836f791535c71ed2 "Bacteria" "Proteobacteria"  
## b43b837314cfb7aef5d3c3fd8e8142b6 "Bacteria" "Proteobacteria"  
## 7eaa2034a21192be6ecfaec001f3fa08 "Bacteria" "Proteobacteria"  
## c378c39c2cfe843318ac7345e6189014 "Bacteria" "Proteobacteria"  
## 6669e651c7a9d2b735e9b7d496508cde "Bacteria" "Proteobacteria"  
## 1a7a971d3bcf21592d1ebabf35d100fd "Bacteria" "Proteobacteria"  
## dc367720df5c1ae8d78019dc83dd2e0b "Bacteria" "Proteobacteria"  
## b8f6759d312f1de655ef951649593ef0 "Bacteria" "Proteobacteria"  
## 21b486ea16b34f5b7ce3c8224c331d5e "Bacteria" "Proteobacteria"  
## ffcd590944755753b1d8ae88273c731f "Bacteria" "Proteobacteria"  
## e522565172c313a3ffddbfc619a2d21b "Bacteria" "Proteobacteria"  
## d96b6207fb8725b32db97bec235ce3d0 "Bacteria" "Proteobacteria"  
## f8c6df3d56ff7649bc52d0aedbc8e048 "Bacteria" "Acidobacteria"   
## 405d0bd8bde3bbf8136655339aaffb32 "Bacteria" "Elusimicrobia"   
## 4f7b6df0faabff63004fd8e4aa84143e "Bacteria" "Spirochaetes"    
## bd450cfd5b93248abf2a4b1ef4e57ae5 "Bacteria" "Spirochaetes"    
## 39832721d381138daa264d1543480827 "Bacteria" "Spirochaetes"    
## 8b9d573892bcf008125b830abb494242 "Bacteria" "Nitrospirae"     
## 22d355b3fc4793261d21a6f9fb219f49 "Bacteria" "Firmicutes"      
## 5b34a5582c8a0efd4e8746a39925b754 "Bacteria" "Firmicutes"      
## 7d4cd07fe04d753bf8bcb57dc27f71b1 "Bacteria" "Firmicutes"      
## 35f15070627d645a49065e8e30004ee4 "Bacteria" "Firmicutes"      
## 7a282fb1eafde33e74e1af68340132cc "Bacteria" "Firmicutes"      
## ba38edc1c02e03da1577a96422af5ea0 "Bacteria" "Firmicutes"      
## 55e81e6a020e5d9dd500a0ac51b0b283 "Bacteria" "Chloroflexi"     
## ad02c5eee2b39f40fac1f608e9a588d2 "Bacteria" "Chloroflexi"     
## fe81a158a7d2c78cdb8d494c150dab85 "Bacteria" "Chloroflexi"     
## 4088b88f122d38e0d64a1691202e7ee6 "Bacteria" "Chloroflexi"     
## 74f297c560f6dad782d11d1b77e88621 "Bacteria" "Chloroflexi"     
## 8c3abd03b35e980141bc63102af4480f "Bacteria" "Chloroflexi"     
## bf71e327691c4854a681e15b28902a68 "Bacteria" "Chloroflexi"     
## 8971ea6436b3f2f9d4f2f4b1bab4ad01 "Bacteria" "[Thermi]"        
## 91d9b2a9eb8359f3b10a4ff82eaac7bb "Bacteria" "Fibrobacteres"   
## 815fc729fe3c00d325ab760f6bb74b08 "Bacteria" "Gemmatimonadetes"
## be014e630e00e5c6e3f0ca87daa86d1b "Bacteria" "Actinobacteria"  
## d443d45b9452b33e2f15317f488a8aff "Bacteria" "Actinobacteria"  
## 2bc3044df4d1da6e21cdc4a5aa7f2d7c "Bacteria" "Actinobacteria"  
## 1da892b315515f65dcfd83beb0e171bc "Bacteria" "Actinobacteria"  
## 84763964b516506d9a5daa198694508a "Bacteria" "Actinobacteria"  
## 4cf10e8585dbc2b18d3aa2def42863cd "Bacteria" "Actinobacteria"  
## 044575c49355d2dc1dc328d7f4cccf07 "Bacteria" "Actinobacteria"  
## 98828518c045dbd013ddf95ed960ff68 "Bacteria" "Actinobacteria"  
## 32b519e9b7a8e3207f070845156855a0 "Bacteria" "Actinobacteria"  
## e9ab2e1d89fdae4700c6740323ae0d91 "Bacteria" "Actinobacteria"  
## 79746a8c7e32d661ecde6164f1de5cbe "Bacteria" "Actinobacteria"  
## c97d71471bfaf2c3e54913809ec72f2a "Bacteria" "Actinobacteria"  
## 9d2d8b251de60fe5dff92e5e0b4ed3f7 "Bacteria" "Actinobacteria"  
## 468b178baa29eebee837710342a0f910 "Bacteria" "Actinobacteria"  
## 49ce92d31439808d0d1bea75a00d5bfc "Bacteria" "Actinobacteria"  
## 537d15ab7624090dc5c79090bd6a167e "Bacteria" "Actinobacteria"  
## 6a817ad430bbcadd29c75840b4fd25c4 "Bacteria" "Actinobacteria"  
## 0a8448ddb119a2aa1e0ae86928097f91 "Bacteria" "Actinobacteria"  
## 62058d158b24b3fbea81b2be7061d67d "Bacteria" "Actinobacteria"  
## f80f713bc2c318c2d2e857fa60324f71 "Bacteria" "Actinobacteria"  
## fb96448a13cbd1b35b97f5ea7c9d9f0c "Bacteria" "Actinobacteria"  
## 492710d4b2c77ae8a3887b6b67edf135 "Bacteria" "Actinobacteria"  
## 399b720f381d18fb6054810664faf3b1 "Bacteria" "Actinobacteria"  
## 4e624224b836599c23297d3c0d738f2c "Bacteria" "Actinobacteria"  
## fe1f9c1511f40357b7ff3f062a9e9a2f "Bacteria" "Actinobacteria"  
## db89f0083e3043374e273f1168399165 "Bacteria" "Actinobacteria"  
## 9606f5b31c4365a210f062af56429ba4 "Bacteria" "Actinobacteria"  
## cf624c989019ccb39a8316fd82969fca "Bacteria" "Actinobacteria"  
## 78bb7782ad610368d38621de127fa83c "Bacteria" "Actinobacteria"  
## 7a4040c73abc580073bdb4eb1d74a33d "Bacteria" "Actinobacteria"  
## a63e98d52785ca8e8af60d0804af5dae "Bacteria" "Actinobacteria"  
## eb07445c23ec6a0baaf838fec7f3f2a5 "Bacteria" "Actinobacteria"  
## ef289d460d88b8bf99288c9ccafa3de4 "Bacteria" "Actinobacteria"  
## d982cb2e9c52d04a131bfd6bfd57143f "Bacteria" "Actinobacteria"  
## f10abcfb58070db144ab557203b15112 "Bacteria" "Actinobacteria"  
## 2e3e409911947f6b58055dac76eafff2 "Bacteria" "Actinobacteria"  
## 6a8e34c34c852052fbb2ef47f31923cf "Bacteria" "Actinobacteria"  
## 69b20ec4a1f82d5d7bfccce73e181144 "Bacteria" "Actinobacteria"  
## 2f3464d9017dbcc3c07539e9e6d031d1 "Bacteria" "Actinobacteria"  
## 19b23b503d10795479f12bed782e37bf "Bacteria" "Actinobacteria"  
## 13c1dc3da2ab678bb67e738463291f41 "Bacteria" "Actinobacteria"  
## 0f7c178d133e189017d861892caf1b54 "Bacteria" "Actinobacteria"  
## 0c416bb1ef62f13288e440253605f1f6 "Bacteria" "Actinobacteria"  
## a9ea27c012d71729be0af434b0135b8f "Bacteria" "Actinobacteria"  
## 9910430d69cf086a7a32730d88e36ca1 "Bacteria" "Actinobacteria"  
## bc5dc688aca3e85050859ccffb837227 "Bacteria" "Actinobacteria"  
## 6cfcb015a00c6f3fb16e6eec63f4a35c "Bacteria" "Actinobacteria"  
## 1034ce7814ed4bb5c4506bc6b75eaa3f "Bacteria" "Actinobacteria"  
## 9dc76e20f768b3449b07c21ff7377623 "Bacteria" "Actinobacteria"  
## 4353875d14dabd7fe11946d21ac50b66 "Bacteria" "Actinobacteria"  
## 1c927fead59f669c939d603634ce60e3 "Bacteria" "Actinobacteria"  
## cc06b4a0146591e922e1f9c019a63485 "Bacteria" "Actinobacteria"  
## c2b4b05dc7cde089c596aaaea2349b57 "Bacteria" "Actinobacteria"  
## c0fcac392fda5b2c85f7eff24b4a08ed "Bacteria" "Actinobacteria"  
## fdc1a7c3ebe3c43c9205147181cadf6b "Bacteria" "Actinobacteria"  
## e229fd918de8f64d13ec2a69bab94a5d "Bacteria" "Actinobacteria"  
## af0d699336503dd28940bf80973df0d1 "Bacteria" "Actinobacteria"  
## 7beb6afb10d4a33729f38eae58eb86fe "Bacteria" "Actinobacteria"  
## 9f213cf8c7852cace5c0bae0997ca479 "Bacteria" "Actinobacteria"  
## e5516025a4d9f48a9fd7248989289b17 "Bacteria" "Cyanobacteria"   
## 265b94ca9e486aa0e39696dbf1004bab "Bacteria" "Cyanobacteria"   
## fc5a4fb7042e9842c36f36e0ab934610 "Bacteria" "Cyanobacteria"   
## c11850f778c3ed2aad77e905a962df9f "Bacteria" "Cyanobacteria"   
## e1defeafac8215315915a82ed015dcb2 "Bacteria" "Cyanobacteria"   
## 4b4b20eeb4a4ccbd441b8d2ef9f31bf7 "Bacteria" "Cyanobacteria"   
## 5575e3a3b9446bc439d3a13064c07e21 "Bacteria" "Cyanobacteria"   
## 565f359611711ce61076b0f3f8eb9453 "Bacteria" "Cyanobacteria"   
## 83196c5429def72c900061a0a8c5b49b "Bacteria" "Cyanobacteria"   
## 0c6f8e3cb66947204cae236072a04a74 "Bacteria" "Cyanobacteria"   
## 2472bec6d09ab949b643cb1a4f41816b "Bacteria" "Cyanobacteria"   
## de5d66672c644945370a3bd62bd2caf4 "Bacteria" "Cyanobacteria"   
## 03ca951e561969caf45da606fde67866 "Bacteria" "Cyanobacteria"   
## d02aa15268aade892ad5dff83af3e7da "Bacteria" "Cyanobacteria"   
## 3cd6ab4607d7c365dfdc11a48bf893c5 "Bacteria" "Cyanobacteria"   
## 48b2489d2a8ef650129b144899cdf302 "Bacteria" "Cyanobacteria"   
## 0040892ff482919cb88018e43a333cca "Bacteria" "Cyanobacteria"   
## a0051aa570b907944f08a912f8bc09fd "Bacteria" "Cyanobacteria"   
## d49b641988fea3844b9de1e6ad26ee98 "Bacteria" "Proteobacteria"  
## 14e8f8943c5595bbea2cca1cc3c383d0 "Bacteria" "Acidobacteria"   
## d9b514bc64139095efef65a654a1d0e2 "Bacteria" "Acidobacteria"   
## f54c0eca0d64aade6c60bbad968da659 "Bacteria" "Nitrospirae"     
## 39e9884255a81dfa04b47a2b11e3ef5b "Bacteria" "Planctomycetes"  
## aa33408e38ea9b07aa856e8e6701b0da "Bacteria" "Acidobacteria"   
## cf7bf8f703a8335c0d3018f4604f1cb6 "Bacteria" "Verrucomicrobia" 
## 31f232781685558bf9d62e35e8f237f9 "Bacteria" "Verrucomicrobia" 
## b8b9f753c83c855cc38aff497e5e89ce "Bacteria" "Verrucomicrobia" 
## 85e29914e803ab4d6fb6602bd6b9ff00 "Bacteria" "Verrucomicrobia" 
## d37b60c688fcca90997aadce4c64d5a9 "Bacteria" "Verrucomicrobia" 
## 107aca9889569069069d195bd8a31697 "Bacteria" "Verrucomicrobia" 
## bd3849fc9106f9cdacb9341795c8cb29 "Bacteria" "Verrucomicrobia" 
## b5d0c6f1b9e8a8302389f77b79dcda85 "Bacteria" "Verrucomicrobia" 
## bd1b5b2bb3a3f6cd721255c7a706da1c "Bacteria" "Verrucomicrobia" 
## b9bad8448867f57e6a14c1a242c48774 "Bacteria" "Verrucomicrobia" 
## b22df4733817d748ec348e7f3e6b33eb "Bacteria" "Verrucomicrobia" 
## 8941145147965d89bfcc4e88c0b9535b "Bacteria" "Verrucomicrobia" 
## 0d9178b0087a618145122137d5f02c9d "Bacteria" "Firmicutes"      
## 1d44015ea379303fcf6b84e6de3b56fe "Bacteria" "Planctomycetes"  
## abbfa75d6cee07b5d473575e6fc31ca6 "Bacteria" "Chlamydiae"      
## ebf9bf8eb6025551e0c72b979eadee03 "Bacteria" "Chlamydiae"      
## 46d7cb3e670b0a7c6be9f9e87b8a9062 "Bacteria" "Chlamydiae"      
## 77ade2a27cd5cf184bc7c566b5e40350 "Bacteria" "Synergistetes"   
## a0cdbcafbb2e9ca1d27ec77bf2e8d58d "Bacteria" "Synergistetes"   
## a79f2d2819aa6abbb25c3d52f0a6d88e "Bacteria" "Deferribacteres" 
## 9640db4284f6de2f96bc6a089999e1d9 "Bacteria" "Spirochaetes"    
##                                  Class                  
## 738f9b43067c64d7dd19a58e16776ca1 "Thermoplasmata"       
## bf3ea7575ee681f6cc071fc10a9b0c9e "Methanobacteria"      
## 81ca8fa4a795e9929b18c343fa7e5d6d "Methanobacteria"      
## fce80713066a40d6d40c78a2bfc701f0 "Fusobacteriia"        
## da2d307acbc750e709821f37106a97ee "Fusobacteriia"        
## ec4dafd949562cb1c67abf1edb908e45 "Fusobacteriia"        
## 937486517cc80db8a7247c8d9cedcb6c "Fusobacteriia"        
## 2960c4868268ab63fffd54d389e709f4 "Mollicutes"           
## b1cc0afab8aabe335f3d2183a8f862a8 "Deinococci"           
## d812033144facb838340db156bc7cddb "Deinococci"           
## a8d5e516d55e0f840a901a1754faf215 "Deinococci"           
## b3f7ce9240052a0925ec9e675b5c5801 "Deinococci"           
## dd2c236c7e7f2b0eca6a81e2ac82e5e9 "Deinococci"           
## f572830d714e07d0b571ccb4029c577b "Deinococci"           
## 12c129f217c4ceeb3f4e6992749ee828 "[Fimbriimonadia]"     
## 1ef109986a98fbad2514a0bdde298328 "Bacteroidia"          
## 550a6c75a980e53ebe63fb821d692cf3 "[Saprospirae]"        
## 08790daac50cd048ed5839225585e108 "[Saprospirae]"        
## 9cbea8ff52e16e14d63f27d5f6f9ee70 "[Saprospirae]"        
## 38876d2e7234ac8c535d914e1b89c7f2 "[Saprospirae]"        
## 937da713490e1d08e8727822deaeb6ca "[Saprospirae]"        
## 32756a7fcc03fdddee0c5b2da35b7940 "Sphingobacteriia"     
## 6ba1a63b03ed1667ddedc0813b737f0d "Bacteroidia"          
## 23f0414ba47f7c7999f913671268837d "Bacteroidia"          
## 5ada85d7be5d55db0cd492bca13b3003 "Bacteroidia"          
## a51c11ce94e4c3cedeeeb25ccda839bb "Bacteroidia"          
## 183f2ec8041f54e28b279213dab7f242 "Bacteroidia"          
## 3ec9a72eea2934c7e20bf5e3840b3935 "Bacteroidia"          
## 6549baa73149f7a4de583300732198e3 "Bacteroidia"          
## f4871a37ef764e383f723e547ad345d3 "Bacteroidia"          
## 12332a0b15374a26f88d178f33975164 "Bacteroidia"          
## 6fa2a60e9fa2afc9bb356bff76e8aea7 "Flavobacteriia"       
## 7ef9ec92fa1dc4d4b175a2590b38c1e3 "Flavobacteriia"       
## 9d0ce3ffd40f17516f311a4f01ce71c3 "Sphingobacteriia"     
## 23ebb02f88264051fb546154a4b76f1f "Sphingobacteriia"     
## 2c2e6c9719c3d353fc8fc4c29277bf3a "Sphingobacteriia"     
## e93b056509933455a642b22131e787f6 "Flavobacteriia"       
## 2f4128d15aa3f31e65bb6be743cf2652 "Flavobacteriia"       
## 82a38739a3d57c68d7488b32235fd9c8 "Flavobacteriia"       
## e87605af38d7adbc36e9bf2ccb4b9ed1 "Flavobacteriia"       
## 675f216a655188ee527413d79502e884 "Flavobacteriia"       
## fd67289a69cb1b8b911c9c0d5aae561c "Flavobacteriia"       
## 0156833a719406d6720169fa7c1a8c4f "Flavobacteriia"       
## 394637d50ed3fa18f7ad4e5f459950bf "Flavobacteriia"       
## 727cd1eebae3ae24468583a5fd29bf40 "Flavobacteriia"       
## fe148c0776bd59b90cb0a4d2f18a7431 "Flavobacteriia"       
## 87b5fc5e91a8d3cc174f4741e97756eb "Flavobacteriia"       
## 97904005472b49b5a729b1f7470c3bce "Flavobacteriia"       
## 0d1d623d430214d67ab7dd50d86923eb "Flavobacteriia"       
## e0534df6ab1aeb8c188f3b0768b7d5ed "Flavobacteriia"       
## 7f356ca83a2db14690a64a74ef25a18a "Bacteroidia"          
## a88bc39d28216b7fea5c260c1eba645b "Bacteroidia"          
## df0e399449afea146ca01aff07d5422e "Bacteroidia"          
## 3abf10c0fb708bc94c3ea4dd299e0970 "Bacteroidia"          
## 22ec7a68d4ffe650f8dd1151196824ae "Bacteroidia"          
## 4431ece8c33501e69a7108763af73b9a "Cytophagia"           
## 943f60dee4de6bf45e42e9305d688b0c "Cytophagia"           
## 2295bf9acbfa418fbcd3b30754f6148e "Cytophagia"           
## 0a8e379dd40b23d151f6392ed1a51934 "Cytophagia"           
## 4ac7304960d351f3fde8c6b271e02cd1 "Cytophagia"           
## 74156312fe86d82180dcebd7fa2f1d3b "Cytophagia"           
## a6c1c1db83cc085b6f4410843de68aec "Cytophagia"           
## abd4e33c5a5b25b15f743da0ba2d47de "Cytophagia"           
## 88063ce6d940ae9490d8f68ebbe70efd "Cytophagia"           
## 76750ffa90fdd5952e8570f9a1fc11f9 "Cytophagia"           
## 0d81c4844619813dd873a65bcf91b75b "Cytophagia"           
## 87ae24a9562a267c0c47df8e04a60f89 "Cytophagia"           
## 5e75d3a55ceb4dc7a55910426de76734 "Cytophagia"           
## c99b81e959d197f32acce3adc9c4fab5 "Cytophagia"           
## 4c16e214394f648bcce3b069ef859388 "Cytophagia"           
## bde4c36da80878e658df02d338931982 "Cytophagia"           
## 61899b1d726126ee51b7335a9e17ea3f "Cytophagia"           
## d2585e354502d89dc5e0a6e923551ec4 "Cytophagia"           
## c5a6d0e5a5aec5fb2aeaea82dea15305 "[Rhodothermi]"        
## 46546f341eac9b2125a8e152eef86d82 "Mollicutes"           
## f39b347d2f6c66682fd9982cae666e88 "Clostridia"           
## 9dbb7cbacf6d05c6f914fd172280c3ff "Clostridia"           
## 8f9ad93911aa5eaeb33b21f8f7c2c45f "Clostridia"           
## d27c33a2c70998d3ea63eb1ff3cb0221 "Clostridia"           
## d5167fdceb8a3baf484e932653cce66b "Clostridia"           
## 92591f68fc9a379243ba99075a0c1a11 "Clostridia"           
## 7b0402e21e2605b6efc8f9ee96439660 "Clostridia"           
## 108ec75ebd3d17a56bfabec9ab334e0e "Clostridia"           
## 49e2fbc314555e9fd5f1accf0fb91af8 "Clostridia"           
## f3f29b983fe8c0dfe37668e9d4ae8bc6 "Clostridia"           
## 569418df588c6249c6525811063aacf5 "Clostridia"           
## 65a75861ea5af532e70ba307bf70a9a9 "Clostridia"           
## bb3291ec469409c1d58c5b0fdc933ec6 "Bacilli"              
## ee9bbcdf5eab5edd0596f444214183cc "Clostridia"           
## 90fe5379a170a7caa71f8f383f485f2b "Clostridia"           
## 0e7f78e494e734305ea59cd0caafa1b8 "Clostridia"           
## 95b83723ec29f8943be9bb7d717c5a4b "Clostridia"           
## 257742c10ede9357a9f59a3217461ae5 "Clostridia"           
## 1db331ef1773d7b27b8e386278202b7e "Clostridia"           
## dd5ce8d0b040693d540cb5aaf1b9fb3b "Clostridia"           
## 9579cc9ad7e64d3305e8aa5e53c667f7 "Clostridia"           
## be88e2bee5866989aa7c16c28646cf50 "Clostridia"           
## 059e847d26f267fa3730d112f3014b1f "Clostridia"           
## 23a5e6774a168faddfac530ac1033388 "Clostridia"           
## f2735c286490a71c359f4d5db6bdd217 "Clostridia"           
## ba0596067c4e680406c82c4baa296538 "Clostridia"           
## f2def42b08374f35a87be49c511de37a "Clostridia"           
## 8302230fee8b0e524dc372e6e97211e1 "Clostridia"           
## 8ac67871377691e5f68c2600870352ec "Clostridia"           
## 75734bf2678c55d2dbbdffa17417ab89 "Clostridia"           
## 198c7b560d46758bcbad890d07833b37 "Clostridia"           
## 75bc33d3f4be73b5221a58ddd6e73798 "Clostridia"           
## 62a7641b0fd611f2b5f56840e4afe298 "Clostridia"           
## 0c438af5dc97a32a49dc6cf46e911b17 "Clostridia"           
## f414562b9ba38395a17b663355f405f8 "Clostridia"           
## f1d10bfa443393cfe67263894c84e566 "Clostridia"           
## d862ff0f8f5c9f39ae13f080aa680bb3 "Clostridia"           
## 702add448b05e3087ea6cecea7dd90b4 "Clostridia"           
## a3a479ce8ea08a480c9a96d6cd9c2f62 "Clostridia"           
## 2546dd1d30f6556190239a0f5c8efad3 "Clostridia"           
## 5891492addacafaf26c9ab65b7c17a3f "Clostridia"           
## 94f2f98ac7d8d5e8ea731c9c3ee48c86 "Clostridia"           
## 61880eb94d6e2c60ff0276bccb67c9ec "Clostridia"           
## 0360a498b5585f9028fa802e6b4f7bf5 "Clostridia"           
## 135ea3e4d147e2cf6e381bd218ca38c2 "Clostridia"           
## 7be1f8896d95573e6ba7523bf6d29546 "Clostridia"           
## ab7e93274f5830e83f60e578976747d3 "Clostridia"           
## 5ad1971e7c113f850929b1752979a1a5 "Clostridia"           
## cb9fe9ff4eb7853282a4d840335b6fc5 "Clostridia"           
## d6377ab8698308388991039193fed9e6 "Erysipelotrichi"      
## c002515d386833fd7c4969a03a9aebb5 "Erysipelotrichi"      
## 99acc08c0d8bfce4ad95740ddf504a83 "Erysipelotrichi"      
## 51c88352cb0925e74ba66a7dd7cde265 "Erysipelotrichi"      
## a71a5fde3bfe18523396fab08f4e474d "Mollicutes"           
## acaa6fe062445b95590d349c619ff73f "Erysipelotrichi"      
## 77be883e73ff901aea64b7487a80e245 "Erysipelotrichi"      
## 07ed27499a5612e2a730ef4d4a95cae9 "Erysipelotrichi"      
## 48ae71b68d6954a54eb355054e9ca62a "Erysipelotrichi"      
## eaa57f77edaae985a5784f41ece4ce33 "Bacilli"              
## da3fd1a55a332ea87aa1da2b633d54b2 "Bacilli"              
## a62e32c83e169200a7222bc5e937b23b "Bacilli"              
## bdbe4504d2313c7e46d1e5a1b4c502f3 "Bacilli"              
## 86599a57e1dcd7a14bdfd8dacbdb29c4 "Bacilli"              
## ff931fa606fa70b98d9cc7339959e1e4 "Bacilli"              
## 26d9efc3df990145f38903f8fcf86546 "Bacilli"              
## c6f61b95201848ba396fcf8f9f393bd8 "Bacilli"              
## 2acd7b47e3bfd5c56047c3922a32dc50 "Bacilli"              
## 56a8dc24218d559971fd66bfbc07b25e "Bacilli"              
## c8b0264dca035066a4f98e8f5f57a1fd "Bacilli"              
## 0ad56849fee2b97ca31f66083120f60a "Bacilli"              
## 0080fef6444702a9598894828d7c6480 "Bacilli"              
## d24f404d0e184ab79cba846971453bcd "Bacilli"              
## 400a504e050fa1e94dbb78a317a91676 "Bacilli"              
## b5d49db9d9ccb60a34050267bfcc36fe "Bacilli"              
## 2c234c87c5882dd4f414aec10fa936c2 "Bacilli"              
## 0f1caf1bbdbe6b2ca659622ee70d0b63 "Bacilli"              
## e5c43f196cbe5ab66faa3c4f467a0886 "Bacilli"              
## 6b085c4046ac5ebe8ef6ac62d791bea5 "Bacilli"              
## c00d929bb5c22936acc74570e3b5bdf6 "Bacilli"              
## 1d05ba400871e661d4b6f5d5221ceaa0 "Bacilli"              
## 4580887b2b9919823d69f37282c7eb68 "Bacilli"              
## 2e398b8d21dc0766b2cf014de5f215f9 "Bacilli"              
## babb2ebb5ca6d5b569dbcd2b4b628198 "Bacilli"              
## bf2c7a63827bc0b6e73780bd35ef1b24 "Bacilli"              
## a5d29f17bd1a64838e0d611fbcdd1ff6 "Bacilli"              
## 3c7e37f4083b0b16aa9124dad86730c7 "Bacilli"              
## 045316716e32037c41e0b163bf4d7f21 "Mollicutes"           
## d8f53497fb4a7d7ece0196fb9f0a6ab4 "Deltaproteobacteria"  
## 5cfcdb0adca683f26388b734166fa45b "Epsilonproteobacteria"
## d372fbcdc973cce384300297bee0478f "Epsilonproteobacteria"
## ae33131a40a790d5a6e096dfe63a89d8 "Epsilonproteobacteria"
## 187e9220f0344b3c3fa9269ef230fc90 "Deltaproteobacteria"  
## 672ee70217e3b5a9235307922a02c7f8 "Deltaproteobacteria"  
## 5e056cc118579d9d7c95fe778b8ea768 "Deltaproteobacteria"  
## 9b487aae59ee8631f146add439f853d2 "Deltaproteobacteria"  
## 1ae19e5736f0e1386f60a9f7c5d78fde "Deltaproteobacteria"  
## 0ab39039498ea9d85c86e8123448534b "Deltaproteobacteria"  
## 653b92284cc9d8af71788389322f0edd "Deltaproteobacteria"  
## e21fc8d6fb72d301fc9c60d5767cce74 "Deltaproteobacteria"  
## e8707202237b30ae28569d165c85bf19 "Deltaproteobacteria"  
## f889b0623697ffab382195032c9ad941 "Deltaproteobacteria"  
## 305ad58751bd60cdfb4c103af7c099f4 "Deltaproteobacteria"  
## 045260d3560e65d1ed7fc1184847d2ab "Deltaproteobacteria"  
## f31d96a0dc85b58019e54c41729a5705 "Gammaproteobacteria"  
## 801ac076ebb43dd3c879924efd470f18 "Gammaproteobacteria"  
## 7c71dd18459d57c725a3ad9ec173d5db "Gammaproteobacteria"  
## 32391b052e2eb6e82b519a21b917701a "Gammaproteobacteria"  
## 90023f83f20dc4626e11297485a2a460 "Gammaproteobacteria"  
## f79e941eee754904cdc3e35d0786a2bd "Gammaproteobacteria"  
## 892d322ffc17d6b4821998ef14e94580 "Gammaproteobacteria"  
## 9b44baa49a601fb4b6c50c312c901778 "Gammaproteobacteria"  
## cbb4db0a376d0da10f3409b324e572b3 "Gammaproteobacteria"  
## 2926f7065c61a289014e2ef920198e41 "Gammaproteobacteria"  
## b90f313249467f3247b2e178108f56c4 "Gammaproteobacteria"  
## 9fb82f32eb82975222f78b04260eaa3a "Gammaproteobacteria"  
## 23ccd8e52a41d7ca1cd3f7d18bb747b7 "Gammaproteobacteria"  
## 2de364e6eaebebbbb28cca6b2ee5f322 "Gammaproteobacteria"  
## 100dda46eb1c9633ba33d459cad7b6d3 "Gammaproteobacteria"  
## 2027d883259942129f4653bb8773ccbb "Gammaproteobacteria"  
## adce59f1751d627ceab8dd97f4d04c6f "Gammaproteobacteria"  
## 4be80be705379fe624bf4f236868c161 "Gammaproteobacteria"  
## 0c8e4b53a95f728aad2fb84bbd346f97 "Gammaproteobacteria"  
## efbb12b0a03e0073ea00bee12f98b36e "Gammaproteobacteria"  
## 1d38cdf4c8a50b1ea96f2156356de988 "Gammaproteobacteria"  
## 19a6bf2bac2f1eda36feda7b342d2fb5 "Gammaproteobacteria"  
## 27105df2940b9391e03c2d80d7f8b4f5 "Gammaproteobacteria"  
## 939aeb8878169f64a49619412a2f63b0 "Gammaproteobacteria"  
## e0e1b66edfc9669ea0d9a6a802bf2788 "Gammaproteobacteria"  
## d89d2a592c1aca630b867e7ccb9e42a6 "Gammaproteobacteria"  
## 5cf7e8ff515a6a5f6104637fd70423c1 "Gammaproteobacteria"  
## 69a578040fb5a9fff8bc026b7909ba83 "Gammaproteobacteria"  
## fbf60a3c4454aa9de8e64561fccc5345 "Gammaproteobacteria"  
## a1d7db2eb229495c2c82b6983acf7e43 "Gammaproteobacteria"  
## 17fad4dc8312a2057293bfc76005b8de "Gammaproteobacteria"  
## 73dc5d7d8e076fd5a6aeddf13f9ef785 "Gammaproteobacteria"  
## 133220fc9566f8823ba6361d973f7e56 "Gammaproteobacteria"  
## 11a0aa4ba2b9f7349d89e260f7091c23 "Gammaproteobacteria"  
## 8a8122d28d426c268bc33a6036ee1201 "Gammaproteobacteria"  
## 56f83521d186287a1334d08d18f63158 "Betaproteobacteria"   
## 8987bf7650d847a8389432b1b97b9076 "Betaproteobacteria"   
## c99ed97ec81f07d7a5bf5e6d39644e78 "Betaproteobacteria"   
## 79d01cf1a57f4ae9b2100a92fc8ccdba "Betaproteobacteria"   
## 49d4b7fc67aed6a6c15b45b14ec2d0bd "Betaproteobacteria"   
## 787102493891f91105723053cb7fa472 "Betaproteobacteria"   
## 83cfc0b49f561f34323bf84f88479fb0 "Gammaproteobacteria"  
## ed4ce9dc264e70619df3ec76f6551fd6 "Gammaproteobacteria"  
## ac967d4c0addb4554c76a32d34fd6c95 "Gammaproteobacteria"  
## 438f1f8281a645f62d60881fd6b0fa57 "Gammaproteobacteria"  
## 7fc26bb3199fb45b03be3a64086369fc "Betaproteobacteria"   
## 69c2a11ae089bcd6b89a7e0e820348a0 "Betaproteobacteria"   
## a1a04d3b99a0830ff52c65019cdbf0ae "Betaproteobacteria"   
## cb8975338b82a1cde52ea64147755a73 "Betaproteobacteria"   
## cbcf57af593627cc223bc600b5fb8318 "Betaproteobacteria"   
## dad64d6402e87f2685829f369810b4da "Betaproteobacteria"   
## 1d4ba0b34502c3002f4e746231e00d5f "Betaproteobacteria"   
## a8f07c39cca53fb138e8007eb22aa6a1 "Betaproteobacteria"   
## 94ea0cf0f0fc7c8f21b14c876a6531e5 "Betaproteobacteria"   
## d689bc688fc4d75a7bb96dae07c80129 "Betaproteobacteria"   
## 085877117ce16b29716cb7211f5bf8e0 "Gammaproteobacteria"  
## 6e8ddec699ec02deed4236f0af079318 "Gammaproteobacteria"  
## dc5b0a8becafb8ce2ca3326fc498464b "Gammaproteobacteria"  
## 1d4f2df9b6265023cd7a291fd570f21d "Gammaproteobacteria"  
## 9b740e8e047c98bb45cd4dc582c1a7f9 "Gammaproteobacteria"  
## b8a850e18c6624af91cd225fbdefa983 "Gammaproteobacteria"  
## e648c38b1b9e6300c7919c49b32f2d6f "Gammaproteobacteria"  
## c1889e2c77161500555ea720c5850b61 "Gammaproteobacteria"  
## 9b6c084f78f830b31a28de8180814ae8 "Gammaproteobacteria"  
## 88242931b35810f68ef8dd396bb1d337 "Gammaproteobacteria"  
## 3e155bea0907cecaf362cac4e87deb3d "Gammaproteobacteria"  
## 5e55605eb003f98493386574e7670725 "Gammaproteobacteria"  
## 14f6c55698300e24e20f0af01fc1362a "Deltaproteobacteria"  
## d59a2064644c08d1dadbbce20f19f527 "Alphaproteobacteria"  
## 20e66d19c6e48da230746eb8df4fbee9 "Alphaproteobacteria"  
## db18ee1beaf8b0931f49185b7e87bb50 "Alphaproteobacteria"  
## 5bddc3e2dd40027af0348e3e496b5ede "Alphaproteobacteria"  
## 98c0af570beeb456ca1529e4b7539b6c "Alphaproteobacteria"  
## 325c677d23378529799356c93bdbf138 "Alphaproteobacteria"  
## 184c1055f8871453d4cfb2e063826c79 "Alphaproteobacteria"  
## 8454ff06fc777ee1792f0a92c0a2a3db "Alphaproteobacteria"  
## 139b3a842bac5a67836f791535c71ed2 "Alphaproteobacteria"  
## b43b837314cfb7aef5d3c3fd8e8142b6 "Alphaproteobacteria"  
## 7eaa2034a21192be6ecfaec001f3fa08 "Alphaproteobacteria"  
## c378c39c2cfe843318ac7345e6189014 "Alphaproteobacteria"  
## 6669e651c7a9d2b735e9b7d496508cde "Alphaproteobacteria"  
## 1a7a971d3bcf21592d1ebabf35d100fd "Alphaproteobacteria"  
## dc367720df5c1ae8d78019dc83dd2e0b "Alphaproteobacteria"  
## b8f6759d312f1de655ef951649593ef0 "Alphaproteobacteria"  
## 21b486ea16b34f5b7ce3c8224c331d5e "Alphaproteobacteria"  
## ffcd590944755753b1d8ae88273c731f "Alphaproteobacteria"  
## e522565172c313a3ffddbfc619a2d21b "Alphaproteobacteria"  
## d96b6207fb8725b32db97bec235ce3d0 "Alphaproteobacteria"  
## f8c6df3d56ff7649bc52d0aedbc8e048 "Acidobacteriia"       
## 405d0bd8bde3bbf8136655339aaffb32 "Elusimicrobia"        
## 4f7b6df0faabff63004fd8e4aa84143e "Spirochaetes"         
## bd450cfd5b93248abf2a4b1ef4e57ae5 "Spirochaetes"         
## 39832721d381138daa264d1543480827 "Spirochaetes"         
## 8b9d573892bcf008125b830abb494242 "Nitrospira"           
## 22d355b3fc4793261d21a6f9fb219f49 "Clostridia"           
## 5b34a5582c8a0efd4e8746a39925b754 "Clostridia"           
## 7d4cd07fe04d753bf8bcb57dc27f71b1 "Bacilli"              
## 35f15070627d645a49065e8e30004ee4 "Bacilli"              
## 7a282fb1eafde33e74e1af68340132cc "Bacilli"              
## ba38edc1c02e03da1577a96422af5ea0 "Bacilli"              
## 55e81e6a020e5d9dd500a0ac51b0b283 "Ktedonobacteria"      
## ad02c5eee2b39f40fac1f608e9a588d2 "Anaerolineae"         
## fe81a158a7d2c78cdb8d494c150dab85 "Anaerolineae"         
## 4088b88f122d38e0d64a1691202e7ee6 "Anaerolineae"         
## 74f297c560f6dad782d11d1b77e88621 "Chloroflexi"          
## 8c3abd03b35e980141bc63102af4480f "Chloroflexi"          
## bf71e327691c4854a681e15b28902a68 "Chloroflexi"          
## 8971ea6436b3f2f9d4f2f4b1bab4ad01 "Deinococci"           
## 91d9b2a9eb8359f3b10a4ff82eaac7bb "Fibrobacteria"        
## 815fc729fe3c00d325ab760f6bb74b08 "Gemmatimonadetes"     
## be014e630e00e5c6e3f0ca87daa86d1b "Coriobacteriia"       
## d443d45b9452b33e2f15317f488a8aff "Coriobacteriia"       
## 2bc3044df4d1da6e21cdc4a5aa7f2d7c "Coriobacteriia"       
## 1da892b315515f65dcfd83beb0e171bc "Coriobacteriia"       
## 84763964b516506d9a5daa198694508a "Coriobacteriia"       
## 4cf10e8585dbc2b18d3aa2def42863cd "Coriobacteriia"       
## 044575c49355d2dc1dc328d7f4cccf07 "Coriobacteriia"       
## 98828518c045dbd013ddf95ed960ff68 "Thermoleophilia"      
## 32b519e9b7a8e3207f070845156855a0 "Thermoleophilia"      
## e9ab2e1d89fdae4700c6740323ae0d91 "Thermoleophilia"      
## 79746a8c7e32d661ecde6164f1de5cbe "Nitriliruptoria"      
## c97d71471bfaf2c3e54913809ec72f2a "Actinobacteria"       
## 9d2d8b251de60fe5dff92e5e0b4ed3f7 "Actinobacteria"       
## 468b178baa29eebee837710342a0f910 "Actinobacteria"       
## 49ce92d31439808d0d1bea75a00d5bfc "Actinobacteria"       
## 537d15ab7624090dc5c79090bd6a167e "Actinobacteria"       
## 6a817ad430bbcadd29c75840b4fd25c4 "Actinobacteria"       
## 0a8448ddb119a2aa1e0ae86928097f91 "Actinobacteria"       
## 62058d158b24b3fbea81b2be7061d67d "Actinobacteria"       
## f80f713bc2c318c2d2e857fa60324f71 "Actinobacteria"       
## fb96448a13cbd1b35b97f5ea7c9d9f0c "Actinobacteria"       
## 492710d4b2c77ae8a3887b6b67edf135 "Actinobacteria"       
## 399b720f381d18fb6054810664faf3b1 "Actinobacteria"       
## 4e624224b836599c23297d3c0d738f2c "Actinobacteria"       
## fe1f9c1511f40357b7ff3f062a9e9a2f "Actinobacteria"       
## db89f0083e3043374e273f1168399165 "Actinobacteria"       
## 9606f5b31c4365a210f062af56429ba4 "Actinobacteria"       
## cf624c989019ccb39a8316fd82969fca "Actinobacteria"       
## 78bb7782ad610368d38621de127fa83c "Actinobacteria"       
## 7a4040c73abc580073bdb4eb1d74a33d "Actinobacteria"       
## a63e98d52785ca8e8af60d0804af5dae "Actinobacteria"       
## eb07445c23ec6a0baaf838fec7f3f2a5 "Actinobacteria"       
## ef289d460d88b8bf99288c9ccafa3de4 "Actinobacteria"       
## d982cb2e9c52d04a131bfd6bfd57143f "Actinobacteria"       
## f10abcfb58070db144ab557203b15112 "Actinobacteria"       
## 2e3e409911947f6b58055dac76eafff2 "Actinobacteria"       
## 6a8e34c34c852052fbb2ef47f31923cf "Actinobacteria"       
## 69b20ec4a1f82d5d7bfccce73e181144 "Actinobacteria"       
## 2f3464d9017dbcc3c07539e9e6d031d1 "Actinobacteria"       
## 19b23b503d10795479f12bed782e37bf "Actinobacteria"       
## 13c1dc3da2ab678bb67e738463291f41 "Actinobacteria"       
## 0f7c178d133e189017d861892caf1b54 "Actinobacteria"       
## 0c416bb1ef62f13288e440253605f1f6 "Actinobacteria"       
## a9ea27c012d71729be0af434b0135b8f "Actinobacteria"       
## 9910430d69cf086a7a32730d88e36ca1 "Actinobacteria"       
## bc5dc688aca3e85050859ccffb837227 "Actinobacteria"       
## 6cfcb015a00c6f3fb16e6eec63f4a35c "Actinobacteria"       
## 1034ce7814ed4bb5c4506bc6b75eaa3f "Actinobacteria"       
## 9dc76e20f768b3449b07c21ff7377623 "Actinobacteria"       
## 4353875d14dabd7fe11946d21ac50b66 "Actinobacteria"       
## 1c927fead59f669c939d603634ce60e3 "Actinobacteria"       
## cc06b4a0146591e922e1f9c019a63485 "Actinobacteria"       
## c2b4b05dc7cde089c596aaaea2349b57 "Actinobacteria"       
## c0fcac392fda5b2c85f7eff24b4a08ed "Actinobacteria"       
## fdc1a7c3ebe3c43c9205147181cadf6b "Actinobacteria"       
## e229fd918de8f64d13ec2a69bab94a5d "Actinobacteria"       
## af0d699336503dd28940bf80973df0d1 "Actinobacteria"       
## 7beb6afb10d4a33729f38eae58eb86fe "Acidimicrobiia"       
## 9f213cf8c7852cace5c0bae0997ca479 "Acidimicrobiia"       
## e5516025a4d9f48a9fd7248989289b17 "Oscillatoriophycideae"
## 265b94ca9e486aa0e39696dbf1004bab "Synechococcophycideae"
## fc5a4fb7042e9842c36f36e0ab934610 "Oscillatoriophycideae"
## c11850f778c3ed2aad77e905a962df9f "Oscillatoriophycideae"
## e1defeafac8215315915a82ed015dcb2 "Nostocophycideae"     
## 4b4b20eeb4a4ccbd441b8d2ef9f31bf7 "Nostocophycideae"     
## 5575e3a3b9446bc439d3a13064c07e21 "Nostocophycideae"     
## 565f359611711ce61076b0f3f8eb9453 "Nostocophycideae"     
## 83196c5429def72c900061a0a8c5b49b "Nostocophycideae"     
## 0c6f8e3cb66947204cae236072a04a74 "Oscillatoriophycideae"
## 2472bec6d09ab949b643cb1a4f41816b "Synechococcophycideae"
## de5d66672c644945370a3bd62bd2caf4 "Synechococcophycideae"
## 03ca951e561969caf45da606fde67866 "Chloroplast"          
## d02aa15268aade892ad5dff83af3e7da "Chloroplast"          
## 3cd6ab4607d7c365dfdc11a48bf893c5 "Oscillatoriophycideae"
## 48b2489d2a8ef650129b144899cdf302 "Chloroplast"          
## 0040892ff482919cb88018e43a333cca "Chloroplast"          
## a0051aa570b907944f08a912f8bc09fd "Chloroplast"          
## d49b641988fea3844b9de1e6ad26ee98 "Alphaproteobacteria"  
## 14e8f8943c5595bbea2cca1cc3c383d0 "Holophagae"           
## d9b514bc64139095efef65a654a1d0e2 "Holophagae"           
## f54c0eca0d64aade6c60bbad968da659 "Nitrospira"           
## 39e9884255a81dfa04b47a2b11e3ef5b "Phycisphaerae"        
## aa33408e38ea9b07aa856e8e6701b0da "Acidobacteriia"       
## cf7bf8f703a8335c0d3018f4604f1cb6 "Opitutae"             
## 31f232781685558bf9d62e35e8f237f9 "Verrucomicrobiae"     
## b8b9f753c83c855cc38aff497e5e89ce "[Spartobacteria]"     
## 85e29914e803ab4d6fb6602bd6b9ff00 "[Spartobacteria]"     
## d37b60c688fcca90997aadce4c64d5a9 "[Pedosphaerae]"       
## 107aca9889569069069d195bd8a31697 "[Spartobacteria]"     
## bd3849fc9106f9cdacb9341795c8cb29 "[Spartobacteria]"     
## b5d0c6f1b9e8a8302389f77b79dcda85 "[Spartobacteria]"     
## bd1b5b2bb3a3f6cd721255c7a706da1c "Verrucomicrobiae"     
## b9bad8448867f57e6a14c1a242c48774 "Verrucomicrobiae"     
## b22df4733817d748ec348e7f3e6b33eb "Verrucomicrobiae"     
## 8941145147965d89bfcc4e88c0b9535b "[Spartobacteria]"     
## 0d9178b0087a618145122137d5f02c9d "Clostridia"           
## 1d44015ea379303fcf6b84e6de3b56fe "Planctomycetia"       
## abbfa75d6cee07b5d473575e6fc31ca6 "Chlamydiia"           
## ebf9bf8eb6025551e0c72b979eadee03 "Chlamydiia"           
## 46d7cb3e670b0a7c6be9f9e87b8a9062 "Chlamydiia"           
## 77ade2a27cd5cf184bc7c566b5e40350 "Synergistia"          
## a0cdbcafbb2e9ca1d27ec77bf2e8d58d "Synergistia"          
## a79f2d2819aa6abbb25c3d52f0a6d88e "Deferribacteres"      
## 9640db4284f6de2f96bc6a089999e1d9 "[Leptospirae]"        
##                                  Order                   
## 738f9b43067c64d7dd19a58e16776ca1 "E2"                    
## bf3ea7575ee681f6cc071fc10a9b0c9e "Methanobacteriales"    
## 81ca8fa4a795e9929b18c343fa7e5d6d "Methanobacteriales"    
## fce80713066a40d6d40c78a2bfc701f0 "Fusobacteriales"       
## da2d307acbc750e709821f37106a97ee "Fusobacteriales"       
## ec4dafd949562cb1c67abf1edb908e45 "Fusobacteriales"       
## 937486517cc80db8a7247c8d9cedcb6c "Fusobacteriales"       
## 2960c4868268ab63fffd54d389e709f4 "Mycoplasmatales"       
## b1cc0afab8aabe335f3d2183a8f862a8 "Deinococcales"         
## d812033144facb838340db156bc7cddb "Deinococcales"         
## a8d5e516d55e0f840a901a1754faf215 "Deinococcales"         
## b3f7ce9240052a0925ec9e675b5c5801 "Deinococcales"         
## dd2c236c7e7f2b0eca6a81e2ac82e5e9 "Deinococcales"         
## f572830d714e07d0b571ccb4029c577b "Deinococcales"         
## 12c129f217c4ceeb3f4e6992749ee828 "[Fimbriimonadales]"    
## 1ef109986a98fbad2514a0bdde298328 "Bacteroidales"         
## 550a6c75a980e53ebe63fb821d692cf3 "[Saprospirales]"       
## 08790daac50cd048ed5839225585e108 "[Saprospirales]"       
## 9cbea8ff52e16e14d63f27d5f6f9ee70 "[Saprospirales]"       
## 38876d2e7234ac8c535d914e1b89c7f2 "[Saprospirales]"       
## 937da713490e1d08e8727822deaeb6ca "[Saprospirales]"       
## 32756a7fcc03fdddee0c5b2da35b7940 "Sphingobacteriales"    
## 6ba1a63b03ed1667ddedc0813b737f0d "Bacteroidales"         
## 23f0414ba47f7c7999f913671268837d "Bacteroidales"         
## 5ada85d7be5d55db0cd492bca13b3003 "Bacteroidales"         
## a51c11ce94e4c3cedeeeb25ccda839bb "Bacteroidales"         
## 183f2ec8041f54e28b279213dab7f242 "Bacteroidales"         
## 3ec9a72eea2934c7e20bf5e3840b3935 "Bacteroidales"         
## 6549baa73149f7a4de583300732198e3 "Bacteroidales"         
## f4871a37ef764e383f723e547ad345d3 "Bacteroidales"         
## 12332a0b15374a26f88d178f33975164 "Bacteroidales"         
## 6fa2a60e9fa2afc9bb356bff76e8aea7 "Flavobacteriales"      
## 7ef9ec92fa1dc4d4b175a2590b38c1e3 "Flavobacteriales"      
## 9d0ce3ffd40f17516f311a4f01ce71c3 "Sphingobacteriales"    
## 23ebb02f88264051fb546154a4b76f1f "Sphingobacteriales"    
## 2c2e6c9719c3d353fc8fc4c29277bf3a "Sphingobacteriales"    
## e93b056509933455a642b22131e787f6 "Flavobacteriales"      
## 2f4128d15aa3f31e65bb6be743cf2652 "Flavobacteriales"      
## 82a38739a3d57c68d7488b32235fd9c8 "Flavobacteriales"      
## e87605af38d7adbc36e9bf2ccb4b9ed1 "Flavobacteriales"      
## 675f216a655188ee527413d79502e884 "Flavobacteriales"      
## fd67289a69cb1b8b911c9c0d5aae561c "Flavobacteriales"      
## 0156833a719406d6720169fa7c1a8c4f "Flavobacteriales"      
## 394637d50ed3fa18f7ad4e5f459950bf "Flavobacteriales"      
## 727cd1eebae3ae24468583a5fd29bf40 "Flavobacteriales"      
## fe148c0776bd59b90cb0a4d2f18a7431 "Flavobacteriales"      
## 87b5fc5e91a8d3cc174f4741e97756eb "Flavobacteriales"      
## 97904005472b49b5a729b1f7470c3bce "Flavobacteriales"      
## 0d1d623d430214d67ab7dd50d86923eb "Flavobacteriales"      
## e0534df6ab1aeb8c188f3b0768b7d5ed "Flavobacteriales"      
## 7f356ca83a2db14690a64a74ef25a18a "Bacteroidales"         
## a88bc39d28216b7fea5c260c1eba645b "Bacteroidales"         
## df0e399449afea146ca01aff07d5422e "Bacteroidales"         
## 3abf10c0fb708bc94c3ea4dd299e0970 "Bacteroidales"         
## 22ec7a68d4ffe650f8dd1151196824ae "Bacteroidales"         
## 4431ece8c33501e69a7108763af73b9a "Cytophagales"          
## 943f60dee4de6bf45e42e9305d688b0c "Cytophagales"          
## 2295bf9acbfa418fbcd3b30754f6148e "Cytophagales"          
## 0a8e379dd40b23d151f6392ed1a51934 "Cytophagales"          
## 4ac7304960d351f3fde8c6b271e02cd1 "Cytophagales"          
## 74156312fe86d82180dcebd7fa2f1d3b "Cytophagales"          
## a6c1c1db83cc085b6f4410843de68aec "Cytophagales"          
## abd4e33c5a5b25b15f743da0ba2d47de "Cytophagales"          
## 88063ce6d940ae9490d8f68ebbe70efd "Cytophagales"          
## 76750ffa90fdd5952e8570f9a1fc11f9 "Cytophagales"          
## 0d81c4844619813dd873a65bcf91b75b "Cytophagales"          
## 87ae24a9562a267c0c47df8e04a60f89 "Cytophagales"          
## 5e75d3a55ceb4dc7a55910426de76734 "Cytophagales"          
## c99b81e959d197f32acce3adc9c4fab5 "Cytophagales"          
## 4c16e214394f648bcce3b069ef859388 "Cytophagales"          
## bde4c36da80878e658df02d338931982 "Cytophagales"          
## 61899b1d726126ee51b7335a9e17ea3f "Cytophagales"          
## d2585e354502d89dc5e0a6e923551ec4 "Cytophagales"          
## c5a6d0e5a5aec5fb2aeaea82dea15305 "[Rhodothermales]"      
## 46546f341eac9b2125a8e152eef86d82 "Anaeroplasmatales"     
## f39b347d2f6c66682fd9982cae666e88 "Clostridiales"         
## 9dbb7cbacf6d05c6f914fd172280c3ff "Clostridiales"         
## 8f9ad93911aa5eaeb33b21f8f7c2c45f "Clostridiales"         
## d27c33a2c70998d3ea63eb1ff3cb0221 "Clostridiales"         
## d5167fdceb8a3baf484e932653cce66b "Clostridiales"         
## 92591f68fc9a379243ba99075a0c1a11 "Halanaerobiales"       
## 7b0402e21e2605b6efc8f9ee96439660 "Clostridiales"         
## 108ec75ebd3d17a56bfabec9ab334e0e "Clostridiales"         
## 49e2fbc314555e9fd5f1accf0fb91af8 "Clostridiales"         
## f3f29b983fe8c0dfe37668e9d4ae8bc6 "Clostridiales"         
## 569418df588c6249c6525811063aacf5 "Clostridiales"         
## 65a75861ea5af532e70ba307bf70a9a9 "Clostridiales"         
## bb3291ec469409c1d58c5b0fdc933ec6 "Haloplasmatales"       
## ee9bbcdf5eab5edd0596f444214183cc "Clostridiales"         
## 90fe5379a170a7caa71f8f383f485f2b "Clostridiales"         
## 0e7f78e494e734305ea59cd0caafa1b8 "Clostridiales"         
## 95b83723ec29f8943be9bb7d717c5a4b "Clostridiales"         
## 257742c10ede9357a9f59a3217461ae5 "Clostridiales"         
## 1db331ef1773d7b27b8e386278202b7e "Clostridiales"         
## dd5ce8d0b040693d540cb5aaf1b9fb3b "Clostridiales"         
## 9579cc9ad7e64d3305e8aa5e53c667f7 "Clostridiales"         
## be88e2bee5866989aa7c16c28646cf50 "Clostridiales"         
## 059e847d26f267fa3730d112f3014b1f "Clostridiales"         
## 23a5e6774a168faddfac530ac1033388 "Clostridiales"         
## f2735c286490a71c359f4d5db6bdd217 "Clostridiales"         
## ba0596067c4e680406c82c4baa296538 "Clostridiales"         
## f2def42b08374f35a87be49c511de37a "Clostridiales"         
## 8302230fee8b0e524dc372e6e97211e1 "Clostridiales"         
## 8ac67871377691e5f68c2600870352ec "Clostridiales"         
## 75734bf2678c55d2dbbdffa17417ab89 "Clostridiales"         
## 198c7b560d46758bcbad890d07833b37 "Clostridiales"         
## 75bc33d3f4be73b5221a58ddd6e73798 "Clostridiales"         
## 62a7641b0fd611f2b5f56840e4afe298 "Clostridiales"         
## 0c438af5dc97a32a49dc6cf46e911b17 "Clostridiales"         
## f414562b9ba38395a17b663355f405f8 "Clostridiales"         
## f1d10bfa443393cfe67263894c84e566 "Clostridiales"         
## d862ff0f8f5c9f39ae13f080aa680bb3 "Clostridiales"         
## 702add448b05e3087ea6cecea7dd90b4 "Clostridiales"         
## a3a479ce8ea08a480c9a96d6cd9c2f62 "Clostridiales"         
## 2546dd1d30f6556190239a0f5c8efad3 "Clostridiales"         
## 5891492addacafaf26c9ab65b7c17a3f "Clostridiales"         
## 94f2f98ac7d8d5e8ea731c9c3ee48c86 "Clostridiales"         
## 61880eb94d6e2c60ff0276bccb67c9ec "Clostridiales"         
## 0360a498b5585f9028fa802e6b4f7bf5 "Clostridiales"         
## 135ea3e4d147e2cf6e381bd218ca38c2 "Clostridiales"         
## 7be1f8896d95573e6ba7523bf6d29546 "Clostridiales"         
## ab7e93274f5830e83f60e578976747d3 "Clostridiales"         
## 5ad1971e7c113f850929b1752979a1a5 "Clostridiales"         
## cb9fe9ff4eb7853282a4d840335b6fc5 "Clostridiales"         
## d6377ab8698308388991039193fed9e6 "Erysipelotrichales"    
## c002515d386833fd7c4969a03a9aebb5 "Erysipelotrichales"    
## 99acc08c0d8bfce4ad95740ddf504a83 "Erysipelotrichales"    
## 51c88352cb0925e74ba66a7dd7cde265 "Erysipelotrichales"    
## a71a5fde3bfe18523396fab08f4e474d "Anaeroplasmatales"     
## acaa6fe062445b95590d349c619ff73f "Erysipelotrichales"    
## 77be883e73ff901aea64b7487a80e245 "Erysipelotrichales"    
## 07ed27499a5612e2a730ef4d4a95cae9 "Erysipelotrichales"    
## 48ae71b68d6954a54eb355054e9ca62a "Erysipelotrichales"    
## eaa57f77edaae985a5784f41ece4ce33 "Lactobacillales"       
## da3fd1a55a332ea87aa1da2b633d54b2 "Lactobacillales"       
## a62e32c83e169200a7222bc5e937b23b "Bacillales"            
## bdbe4504d2313c7e46d1e5a1b4c502f3 "Bacillales"            
## 86599a57e1dcd7a14bdfd8dacbdb29c4 "Bacillales"            
## ff931fa606fa70b98d9cc7339959e1e4 "Bacillales"            
## 26d9efc3df990145f38903f8fcf86546 "Bacillales"            
## c6f61b95201848ba396fcf8f9f393bd8 "Bacillales"            
## 2acd7b47e3bfd5c56047c3922a32dc50 "Bacillales"            
## 56a8dc24218d559971fd66bfbc07b25e "Bacillales"            
## c8b0264dca035066a4f98e8f5f57a1fd "Bacillales"            
## 0ad56849fee2b97ca31f66083120f60a "Bacillales"            
## 0080fef6444702a9598894828d7c6480 "Bacillales"            
## d24f404d0e184ab79cba846971453bcd "Bacillales"            
## 400a504e050fa1e94dbb78a317a91676 "Lactobacillales"       
## b5d49db9d9ccb60a34050267bfcc36fe "Lactobacillales"       
## 2c234c87c5882dd4f414aec10fa936c2 "Lactobacillales"       
## 0f1caf1bbdbe6b2ca659622ee70d0b63 "Lactobacillales"       
## e5c43f196cbe5ab66faa3c4f467a0886 "Lactobacillales"       
## 6b085c4046ac5ebe8ef6ac62d791bea5 "Lactobacillales"       
## c00d929bb5c22936acc74570e3b5bdf6 "Lactobacillales"       
## 1d05ba400871e661d4b6f5d5221ceaa0 "Lactobacillales"       
## 4580887b2b9919823d69f37282c7eb68 "Lactobacillales"       
## 2e398b8d21dc0766b2cf014de5f215f9 "Lactobacillales"       
## babb2ebb5ca6d5b569dbcd2b4b628198 "Lactobacillales"       
## bf2c7a63827bc0b6e73780bd35ef1b24 "Lactobacillales"       
## a5d29f17bd1a64838e0d611fbcdd1ff6 "Lactobacillales"       
## 3c7e37f4083b0b16aa9124dad86730c7 "Bacillales"            
## 045316716e32037c41e0b163bf4d7f21 "Acholeplasmatales"     
## d8f53497fb4a7d7ece0196fb9f0a6ab4 "Bdellovibrionales"     
## 5cfcdb0adca683f26388b734166fa45b "Campylobacterales"     
## d372fbcdc973cce384300297bee0478f "Campylobacterales"     
## ae33131a40a790d5a6e096dfe63a89d8 "Campylobacterales"     
## 187e9220f0344b3c3fa9269ef230fc90 "Desulfuromonadales"    
## 672ee70217e3b5a9235307922a02c7f8 "Bdellovibrionales"     
## 5e056cc118579d9d7c95fe778b8ea768 "Myxococcales"          
## 9b487aae59ee8631f146add439f853d2 "Myxococcales"          
## 1ae19e5736f0e1386f60a9f7c5d78fde "Myxococcales"          
## 0ab39039498ea9d85c86e8123448534b "Myxococcales"          
## 653b92284cc9d8af71788389322f0edd "Myxococcales"          
## e21fc8d6fb72d301fc9c60d5767cce74 "Desulfovibrionales"    
## e8707202237b30ae28569d165c85bf19 "Desulfovibrionales"    
## f889b0623697ffab382195032c9ad941 "Desulfovibrionales"    
## 305ad58751bd60cdfb4c103af7c099f4 "Desulfobacterales"     
## 045260d3560e65d1ed7fc1184847d2ab "Myxococcales"          
## f31d96a0dc85b58019e54c41729a5705 "Alteromonadales"       
## 801ac076ebb43dd3c879924efd470f18 "Methylococcales"       
## 7c71dd18459d57c725a3ad9ec173d5db "Methylococcales"       
## 32391b052e2eb6e82b519a21b917701a "Cardiobacteriales"     
## 90023f83f20dc4626e11297485a2a460 "Oceanospirillales"     
## f79e941eee754904cdc3e35d0786a2bd "Alteromonadales"       
## 892d322ffc17d6b4821998ef14e94580 "Oceanospirillales"     
## 9b44baa49a601fb4b6c50c312c901778 "Pseudomonadales"       
## cbb4db0a376d0da10f3409b324e572b3 "Enterobacteriales"     
## 2926f7065c61a289014e2ef920198e41 "Pseudomonadales"       
## b90f313249467f3247b2e178108f56c4 "Alteromonadales"       
## 9fb82f32eb82975222f78b04260eaa3a "Alteromonadales"       
## 23ccd8e52a41d7ca1cd3f7d18bb747b7 "Oceanospirillales"     
## 2de364e6eaebebbbb28cca6b2ee5f322 "Oceanospirillales"     
## 100dda46eb1c9633ba33d459cad7b6d3 "Chromatiales"          
## 2027d883259942129f4653bb8773ccbb "Oceanospirillales"     
## adce59f1751d627ceab8dd97f4d04c6f "Pseudomonadales"       
## 4be80be705379fe624bf4f236868c161 "Pseudomonadales"       
## 0c8e4b53a95f728aad2fb84bbd346f97 "Alteromonadales"       
## efbb12b0a03e0073ea00bee12f98b36e "Alteromonadales"       
## 1d38cdf4c8a50b1ea96f2156356de988 "Enterobacteriales"     
## 19a6bf2bac2f1eda36feda7b342d2fb5 "Enterobacteriales"     
## 27105df2940b9391e03c2d80d7f8b4f5 "Enterobacteriales"     
## 939aeb8878169f64a49619412a2f63b0 "Aeromonadales"         
## e0e1b66edfc9669ea0d9a6a802bf2788 "Vibrionales"           
## d89d2a592c1aca630b867e7ccb9e42a6 "Vibrionales"           
## 5cf7e8ff515a6a5f6104637fd70423c1 "Vibrionales"           
## 69a578040fb5a9fff8bc026b7909ba83 "Vibrionales"           
## fbf60a3c4454aa9de8e64561fccc5345 "Alteromonadales"       
## a1d7db2eb229495c2c82b6983acf7e43 "Aeromonadales"         
## 17fad4dc8312a2057293bfc76005b8de "Aeromonadales"         
## 73dc5d7d8e076fd5a6aeddf13f9ef785 "Xanthomonadales"       
## 133220fc9566f8823ba6361d973f7e56 "Xanthomonadales"       
## 11a0aa4ba2b9f7349d89e260f7091c23 "Legionellales"         
## 8a8122d28d426c268bc33a6036ee1201 "Legionellales"         
## 56f83521d186287a1334d08d18f63158 "Nitrosomonadales"      
## 8987bf7650d847a8389432b1b97b9076 "Methylophilales"       
## c99ed97ec81f07d7a5bf5e6d39644e78 "Rhodocyclales"         
## 79d01cf1a57f4ae9b2100a92fc8ccdba "Neisseriales"          
## 49d4b7fc67aed6a6c15b45b14ec2d0bd "Burkholderiales"       
## 787102493891f91105723053cb7fa472 "Burkholderiales"       
## 83cfc0b49f561f34323bf84f88479fb0 "Pasteurellales"        
## ed4ce9dc264e70619df3ec76f6551fd6 "Pasteurellales"        
## ac967d4c0addb4554c76a32d34fd6c95 "Pasteurellales"        
## 438f1f8281a645f62d60881fd6b0fa57 "Pasteurellales"        
## 7fc26bb3199fb45b03be3a64086369fc "Burkholderiales"       
## 69c2a11ae089bcd6b89a7e0e820348a0 "Burkholderiales"       
## a1a04d3b99a0830ff52c65019cdbf0ae "Burkholderiales"       
## cb8975338b82a1cde52ea64147755a73 "Burkholderiales"       
## cbcf57af593627cc223bc600b5fb8318 "Burkholderiales"       
## dad64d6402e87f2685829f369810b4da "Burkholderiales"       
## 1d4ba0b34502c3002f4e746231e00d5f "Procabacteriales"      
## a8f07c39cca53fb138e8007eb22aa6a1 "Neisseriales"          
## 94ea0cf0f0fc7c8f21b14c876a6531e5 "Neisseriales"          
## d689bc688fc4d75a7bb96dae07c80129 "Burkholderiales"       
## 085877117ce16b29716cb7211f5bf8e0 "Xanthomonadales"       
## 6e8ddec699ec02deed4236f0af079318 "Xanthomonadales"       
## dc5b0a8becafb8ce2ca3326fc498464b "Pseudomonadales"       
## 1d4f2df9b6265023cd7a291fd570f21d "Pseudomonadales"       
## 9b740e8e047c98bb45cd4dc582c1a7f9 "Pseudomonadales"       
## b8a850e18c6624af91cd225fbdefa983 "Xanthomonadales"       
## e648c38b1b9e6300c7919c49b32f2d6f "Xanthomonadales"       
## c1889e2c77161500555ea720c5850b61 "Xanthomonadales"       
## 9b6c084f78f830b31a28de8180814ae8 "Xanthomonadales"       
## 88242931b35810f68ef8dd396bb1d337 "Xanthomonadales"       
## 3e155bea0907cecaf362cac4e87deb3d "Xanthomonadales"       
## 5e55605eb003f98493386574e7670725 "Xanthomonadales"       
## 14f6c55698300e24e20f0af01fc1362a "Syntrophobacterales"   
## d59a2064644c08d1dadbbce20f19f527 "Rhodospirillales"      
## 20e66d19c6e48da230746eb8df4fbee9 "Rhodospirillales"      
## db18ee1beaf8b0931f49185b7e87bb50 "Rhodospirillales"      
## 5bddc3e2dd40027af0348e3e496b5ede "Rhizobiales"           
## 98c0af570beeb456ca1529e4b7539b6c "Rhizobiales"           
## 325c677d23378529799356c93bdbf138 "Rhizobiales"           
## 184c1055f8871453d4cfb2e063826c79 "Rhizobiales"           
## 8454ff06fc777ee1792f0a92c0a2a3db "Rhizobiales"           
## 139b3a842bac5a67836f791535c71ed2 "Rhizobiales"           
## b43b837314cfb7aef5d3c3fd8e8142b6 "Rhizobiales"           
## 7eaa2034a21192be6ecfaec001f3fa08 "Caulobacterales"       
## c378c39c2cfe843318ac7345e6189014 "Caulobacterales"       
## 6669e651c7a9d2b735e9b7d496508cde "Caulobacterales"       
## 1a7a971d3bcf21592d1ebabf35d100fd "Caulobacterales"       
## dc367720df5c1ae8d78019dc83dd2e0b "Sphingomonadales"      
## b8f6759d312f1de655ef951649593ef0 "Sphingomonadales"      
## 21b486ea16b34f5b7ce3c8224c331d5e "Sphingomonadales"      
## ffcd590944755753b1d8ae88273c731f "Rhodospirillales"      
## e522565172c313a3ffddbfc619a2d21b "Rickettsiales"         
## d96b6207fb8725b32db97bec235ce3d0 "Rhodospirillales"      
## f8c6df3d56ff7649bc52d0aedbc8e048 "Acidobacteriales"      
## 405d0bd8bde3bbf8136655339aaffb32 "Elusimicrobiales"      
## 4f7b6df0faabff63004fd8e4aa84143e "Spirochaetales"        
## bd450cfd5b93248abf2a4b1ef4e57ae5 "Spirochaetales"        
## 39832721d381138daa264d1543480827 "[Borreliales]"         
## 8b9d573892bcf008125b830abb494242 "Nitrospirales"         
## 22d355b3fc4793261d21a6f9fb219f49 "Thermoanaerobacterales"
## 5b34a5582c8a0efd4e8746a39925b754 "Clostridiales"         
## 7d4cd07fe04d753bf8bcb57dc27f71b1 "Bacillales"            
## 35f15070627d645a49065e8e30004ee4 "Bacillales"            
## 7a282fb1eafde33e74e1af68340132cc "Bacillales"            
## ba38edc1c02e03da1577a96422af5ea0 "Bacillales"            
## 55e81e6a020e5d9dd500a0ac51b0b283 "Ktedonobacterales"     
## ad02c5eee2b39f40fac1f608e9a588d2 "Anaerolineales"        
## fe81a158a7d2c78cdb8d494c150dab85 "Anaerolineales"        
## 4088b88f122d38e0d64a1691202e7ee6 "Caldilineales"         
## 74f297c560f6dad782d11d1b77e88621 "Chloroflexales"        
## 8c3abd03b35e980141bc63102af4480f "Chloroflexales"        
## bf71e327691c4854a681e15b28902a68 "[Roseiflexales]"       
## 8971ea6436b3f2f9d4f2f4b1bab4ad01 "Thermales"             
## 91d9b2a9eb8359f3b10a4ff82eaac7bb "Fibrobacterales"       
## 815fc729fe3c00d325ab760f6bb74b08 "Gemmatimonadales"      
## be014e630e00e5c6e3f0ca87daa86d1b "Coriobacteriales"      
## d443d45b9452b33e2f15317f488a8aff "Coriobacteriales"      
## 2bc3044df4d1da6e21cdc4a5aa7f2d7c "Coriobacteriales"      
## 1da892b315515f65dcfd83beb0e171bc "Coriobacteriales"      
## 84763964b516506d9a5daa198694508a "Coriobacteriales"      
## 4cf10e8585dbc2b18d3aa2def42863cd "Coriobacteriales"      
## 044575c49355d2dc1dc328d7f4cccf07 "Coriobacteriales"      
## 98828518c045dbd013ddf95ed960ff68 "Gaiellales"            
## 32b519e9b7a8e3207f070845156855a0 "Solirubrobacterales"   
## e9ab2e1d89fdae4700c6740323ae0d91 "Solirubrobacterales"   
## 79746a8c7e32d661ecde6164f1de5cbe "Nitriliruptorales"     
## c97d71471bfaf2c3e54913809ec72f2a "Actinomycetales"       
## 9d2d8b251de60fe5dff92e5e0b4ed3f7 "Actinomycetales"       
## 468b178baa29eebee837710342a0f910 "Actinomycetales"       
## 49ce92d31439808d0d1bea75a00d5bfc "Actinomycetales"       
## 537d15ab7624090dc5c79090bd6a167e "Actinomycetales"       
## 6a817ad430bbcadd29c75840b4fd25c4 "Actinomycetales"       
## 0a8448ddb119a2aa1e0ae86928097f91 "Actinomycetales"       
## 62058d158b24b3fbea81b2be7061d67d "Actinomycetales"       
## f80f713bc2c318c2d2e857fa60324f71 "Actinomycetales"       
## fb96448a13cbd1b35b97f5ea7c9d9f0c "Actinomycetales"       
## 492710d4b2c77ae8a3887b6b67edf135 "Actinomycetales"       
## 399b720f381d18fb6054810664faf3b1 "Actinomycetales"       
## 4e624224b836599c23297d3c0d738f2c "Actinomycetales"       
## fe1f9c1511f40357b7ff3f062a9e9a2f "Actinomycetales"       
## db89f0083e3043374e273f1168399165 "Actinomycetales"       
## 9606f5b31c4365a210f062af56429ba4 "Actinomycetales"       
## cf624c989019ccb39a8316fd82969fca "Actinomycetales"       
## 78bb7782ad610368d38621de127fa83c "Actinomycetales"       
## 7a4040c73abc580073bdb4eb1d74a33d "Actinomycetales"       
## a63e98d52785ca8e8af60d0804af5dae "Actinomycetales"       
## eb07445c23ec6a0baaf838fec7f3f2a5 "Actinomycetales"       
## ef289d460d88b8bf99288c9ccafa3de4 "Actinomycetales"       
## d982cb2e9c52d04a131bfd6bfd57143f "Actinomycetales"       
## f10abcfb58070db144ab557203b15112 "Actinomycetales"       
## 2e3e409911947f6b58055dac76eafff2 "Bifidobacteriales"     
## 6a8e34c34c852052fbb2ef47f31923cf "Bifidobacteriales"     
## 69b20ec4a1f82d5d7bfccce73e181144 "Bifidobacteriales"     
## 2f3464d9017dbcc3c07539e9e6d031d1 "Actinomycetales"       
## 19b23b503d10795479f12bed782e37bf "Actinomycetales"       
## 13c1dc3da2ab678bb67e738463291f41 "Actinomycetales"       
## 0f7c178d133e189017d861892caf1b54 "Actinomycetales"       
## 0c416bb1ef62f13288e440253605f1f6 "Actinomycetales"       
## a9ea27c012d71729be0af434b0135b8f "Actinomycetales"       
## 9910430d69cf086a7a32730d88e36ca1 "Actinomycetales"       
## bc5dc688aca3e85050859ccffb837227 "Actinomycetales"       
## 6cfcb015a00c6f3fb16e6eec63f4a35c "Actinomycetales"       
## 1034ce7814ed4bb5c4506bc6b75eaa3f "Actinomycetales"       
## 9dc76e20f768b3449b07c21ff7377623 "Actinomycetales"       
## 4353875d14dabd7fe11946d21ac50b66 "Actinomycetales"       
## 1c927fead59f669c939d603634ce60e3 "Actinomycetales"       
## cc06b4a0146591e922e1f9c019a63485 "Actinomycetales"       
## c2b4b05dc7cde089c596aaaea2349b57 "Actinomycetales"       
## c0fcac392fda5b2c85f7eff24b4a08ed "Actinomycetales"       
## fdc1a7c3ebe3c43c9205147181cadf6b "Actinomycetales"       
## e229fd918de8f64d13ec2a69bab94a5d "Actinomycetales"       
## af0d699336503dd28940bf80973df0d1 "Actinomycetales"       
## 7beb6afb10d4a33729f38eae58eb86fe "Acidimicrobiales"      
## 9f213cf8c7852cace5c0bae0997ca479 "Acidimicrobiales"      
## e5516025a4d9f48a9fd7248989289b17 "Chroococcales"         
## 265b94ca9e486aa0e39696dbf1004bab "Pseudanabaenales"      
## fc5a4fb7042e9842c36f36e0ab934610 "Chroococcales"         
## c11850f778c3ed2aad77e905a962df9f "Chroococcales"         
## e1defeafac8215315915a82ed015dcb2 "Nostocales"            
## 4b4b20eeb4a4ccbd441b8d2ef9f31bf7 "Nostocales"            
## 5575e3a3b9446bc439d3a13064c07e21 "Nostocales"            
## 565f359611711ce61076b0f3f8eb9453 "Nostocales"            
## 83196c5429def72c900061a0a8c5b49b "Nostocales"            
## 0c6f8e3cb66947204cae236072a04a74 "Oscillatoriales"       
## 2472bec6d09ab949b643cb1a4f41816b "Pseudanabaenales"      
## de5d66672c644945370a3bd62bd2caf4 "Pseudanabaenales"      
## 03ca951e561969caf45da606fde67866 "Chlorophyta"           
## d02aa15268aade892ad5dff83af3e7da "Chlorophyta"           
## 3cd6ab4607d7c365dfdc11a48bf893c5 "Oscillatoriales"       
## 48b2489d2a8ef650129b144899cdf302 "Chlorophyta"           
## 0040892ff482919cb88018e43a333cca "Chlorophyta"           
## a0051aa570b907944f08a912f8bc09fd "Chlorophyta"           
## d49b641988fea3844b9de1e6ad26ee98 "Rhizobiales"           
## 14e8f8943c5595bbea2cca1cc3c383d0 "Holophagales"          
## d9b514bc64139095efef65a654a1d0e2 "Holophagales"          
## f54c0eca0d64aade6c60bbad968da659 "Nitrospirales"         
## 39e9884255a81dfa04b47a2b11e3ef5b "Phycisphaerales"       
## aa33408e38ea9b07aa856e8e6701b0da "Acidobacteriales"      
## cf7bf8f703a8335c0d3018f4604f1cb6 "Opitutales"            
## 31f232781685558bf9d62e35e8f237f9 "Verrucomicrobiales"    
## b8b9f753c83c855cc38aff497e5e89ce "[Chthoniobacterales]"  
## 85e29914e803ab4d6fb6602bd6b9ff00 "[Chthoniobacterales]"  
## d37b60c688fcca90997aadce4c64d5a9 "[Pedosphaerales]"      
## 107aca9889569069069d195bd8a31697 "[Chthoniobacterales]"  
## bd3849fc9106f9cdacb9341795c8cb29 "[Chthoniobacterales]"  
## b5d0c6f1b9e8a8302389f77b79dcda85 "[Chthoniobacterales]"  
## bd1b5b2bb3a3f6cd721255c7a706da1c "Verrucomicrobiales"    
## b9bad8448867f57e6a14c1a242c48774 "Verrucomicrobiales"    
## b22df4733817d748ec348e7f3e6b33eb "Verrucomicrobiales"    
## 8941145147965d89bfcc4e88c0b9535b "[Chthoniobacterales]"  
## 0d9178b0087a618145122137d5f02c9d "Thermoanaerobacterales"
## 1d44015ea379303fcf6b84e6de3b56fe "Gemmatales"            
## abbfa75d6cee07b5d473575e6fc31ca6 "Chlamydiales"          
## ebf9bf8eb6025551e0c72b979eadee03 "Chlamydiales"          
## 46d7cb3e670b0a7c6be9f9e87b8a9062 "Chlamydiales"          
## 77ade2a27cd5cf184bc7c566b5e40350 "Synergistales"         
## a0cdbcafbb2e9ca1d27ec77bf2e8d58d "Synergistales"         
## a79f2d2819aa6abbb25c3d52f0a6d88e "Deferribacterales"     
## 9640db4284f6de2f96bc6a089999e1d9 "[Leptospirales]"       
##                                  Family                      
## 738f9b43067c64d7dd19a58e16776ca1 "[Methanomassiliicoccaceae]"
## bf3ea7575ee681f6cc071fc10a9b0c9e "Methanobacteriaceae"       
## 81ca8fa4a795e9929b18c343fa7e5d6d "Methanobacteriaceae"       
## fce80713066a40d6d40c78a2bfc701f0 "Fusobacteriaceae"          
## da2d307acbc750e709821f37106a97ee "Leptotrichiaceae"          
## ec4dafd949562cb1c67abf1edb908e45 "Leptotrichiaceae"          
## 937486517cc80db8a7247c8d9cedcb6c "Leptotrichiaceae"          
## 2960c4868268ab63fffd54d389e709f4 "Mycoplasmataceae"          
## b1cc0afab8aabe335f3d2183a8f862a8 "Trueperaceae"              
## d812033144facb838340db156bc7cddb "Trueperaceae"              
## a8d5e516d55e0f840a901a1754faf215 "Deinococcaceae"            
## b3f7ce9240052a0925ec9e675b5c5801 "Deinococcaceae"            
## dd2c236c7e7f2b0eca6a81e2ac82e5e9 "Deinococcaceae"            
## f572830d714e07d0b571ccb4029c577b "Deinococcaceae"            
## 12c129f217c4ceeb3f4e6992749ee828 "[Fimbriimonadaceae]"       
## 1ef109986a98fbad2514a0bdde298328 "[Odoribacteraceae]"        
## 550a6c75a980e53ebe63fb821d692cf3 "Chitinophagaceae"          
## 08790daac50cd048ed5839225585e108 "Chitinophagaceae"          
## 9cbea8ff52e16e14d63f27d5f6f9ee70 "Chitinophagaceae"          
## 38876d2e7234ac8c535d914e1b89c7f2 "Chitinophagaceae"          
## 937da713490e1d08e8727822deaeb6ca "Chitinophagaceae"          
## 32756a7fcc03fdddee0c5b2da35b7940 "Sphingobacteriaceae"       
## 6ba1a63b03ed1667ddedc0813b737f0d "Rikenellaceae"             
## 23f0414ba47f7c7999f913671268837d "Rikenellaceae"             
## 5ada85d7be5d55db0cd492bca13b3003 "Marinilabiaceae"           
## a51c11ce94e4c3cedeeeb25ccda839bb "Bacteroidaceae"            
## 183f2ec8041f54e28b279213dab7f242 "[Paraprevotellaceae]"      
## 3ec9a72eea2934c7e20bf5e3840b3935 "Porphyromonadaceae"        
## 6549baa73149f7a4de583300732198e3 "Porphyromonadaceae"        
## f4871a37ef764e383f723e547ad345d3 "Porphyromonadaceae"        
## 12332a0b15374a26f88d178f33975164 "[Barnesiellaceae]"         
## 6fa2a60e9fa2afc9bb356bff76e8aea7 "Cryomorphaceae"            
## 7ef9ec92fa1dc4d4b175a2590b38c1e3 "Cryomorphaceae"            
## 9d0ce3ffd40f17516f311a4f01ce71c3 "Sphingobacteriaceae"       
## 23ebb02f88264051fb546154a4b76f1f "Sphingobacteriaceae"       
## 2c2e6c9719c3d353fc8fc4c29277bf3a "Sphingobacteriaceae"       
## e93b056509933455a642b22131e787f6 "Flavobacteriaceae"         
## 2f4128d15aa3f31e65bb6be743cf2652 "Flavobacteriaceae"         
## 82a38739a3d57c68d7488b32235fd9c8 "Flavobacteriaceae"         
## e87605af38d7adbc36e9bf2ccb4b9ed1 "Flavobacteriaceae"         
## 675f216a655188ee527413d79502e884 "Flavobacteriaceae"         
## fd67289a69cb1b8b911c9c0d5aae561c "Flavobacteriaceae"         
## 0156833a719406d6720169fa7c1a8c4f "Flavobacteriaceae"         
## 394637d50ed3fa18f7ad4e5f459950bf "Flavobacteriaceae"         
## 727cd1eebae3ae24468583a5fd29bf40 "Flavobacteriaceae"         
## fe148c0776bd59b90cb0a4d2f18a7431 "Flavobacteriaceae"         
## 87b5fc5e91a8d3cc174f4741e97756eb "[Weeksellaceae]"           
## 97904005472b49b5a729b1f7470c3bce "[Weeksellaceae]"           
## 0d1d623d430214d67ab7dd50d86923eb "[Weeksellaceae]"           
## e0534df6ab1aeb8c188f3b0768b7d5ed "[Weeksellaceae]"           
## 7f356ca83a2db14690a64a74ef25a18a "Bacteroidaceae"            
## a88bc39d28216b7fea5c260c1eba645b "[Paraprevotellaceae]"      
## df0e399449afea146ca01aff07d5422e "[Paraprevotellaceae]"      
## 3abf10c0fb708bc94c3ea4dd299e0970 "Prevotellaceae"            
## 22ec7a68d4ffe650f8dd1151196824ae "[Paraprevotellaceae]"      
## 4431ece8c33501e69a7108763af73b9a "Cytophagaceae"             
## 943f60dee4de6bf45e42e9305d688b0c "Cytophagaceae"             
## 2295bf9acbfa418fbcd3b30754f6148e "Cytophagaceae"             
## 0a8e379dd40b23d151f6392ed1a51934 "Flammeovirgaceae"          
## 4ac7304960d351f3fde8c6b271e02cd1 "Cytophagaceae"             
## 74156312fe86d82180dcebd7fa2f1d3b "Flammeovirgaceae"          
## a6c1c1db83cc085b6f4410843de68aec "Flammeovirgaceae"          
## abd4e33c5a5b25b15f743da0ba2d47de "Flammeovirgaceae"          
## 88063ce6d940ae9490d8f68ebbe70efd "Cyclobacteriaceae"         
## 76750ffa90fdd5952e8570f9a1fc11f9 "Cyclobacteriaceae"         
## 0d81c4844619813dd873a65bcf91b75b "Cyclobacteriaceae"         
## 87ae24a9562a267c0c47df8e04a60f89 "Cyclobacteriaceae"         
## 5e75d3a55ceb4dc7a55910426de76734 "Cytophagaceae"             
## c99b81e959d197f32acce3adc9c4fab5 "Cytophagaceae"             
## 4c16e214394f648bcce3b069ef859388 "Cytophagaceae"             
## bde4c36da80878e658df02d338931982 "Cytophagaceae"             
## 61899b1d726126ee51b7335a9e17ea3f "Cytophagaceae"             
## d2585e354502d89dc5e0a6e923551ec4 "Cytophagaceae"             
## c5a6d0e5a5aec5fb2aeaea82dea15305 "Rhodothermaceae"           
## 46546f341eac9b2125a8e152eef86d82 "Anaeroplasmataceae"        
## f39b347d2f6c66682fd9982cae666e88 "Veillonellaceae"           
## 9dbb7cbacf6d05c6f914fd172280c3ff "Veillonellaceae"           
## 8f9ad93911aa5eaeb33b21f8f7c2c45f "Eubacteriaceae"            
## d27c33a2c70998d3ea63eb1ff3cb0221 "Peptococcaceae"            
## d5167fdceb8a3baf484e932653cce66b "Peptococcaceae"            
## 92591f68fc9a379243ba99075a0c1a11 "Halanaerobiaceae"          
## 7b0402e21e2605b6efc8f9ee96439660 "[Tissierellaceae]"         
## 108ec75ebd3d17a56bfabec9ab334e0e "[Tissierellaceae]"         
## 49e2fbc314555e9fd5f1accf0fb91af8 "[Tissierellaceae]"         
## f3f29b983fe8c0dfe37668e9d4ae8bc6 "[Tissierellaceae]"         
## 569418df588c6249c6525811063aacf5 "[Tissierellaceae]"         
## 65a75861ea5af532e70ba307bf70a9a9 "[Tissierellaceae]"         
## bb3291ec469409c1d58c5b0fdc933ec6 "Haloplasmataceae"          
## ee9bbcdf5eab5edd0596f444214183cc "[Tissierellaceae]"         
## 90fe5379a170a7caa71f8f383f485f2b "[Tissierellaceae]"         
## 0e7f78e494e734305ea59cd0caafa1b8 "Peptostreptococcaceae"     
## 95b83723ec29f8943be9bb7d717c5a4b "Peptostreptococcaceae"     
## 257742c10ede9357a9f59a3217461ae5 "Peptostreptococcaceae"     
## 1db331ef1773d7b27b8e386278202b7e "Peptostreptococcaceae"     
## dd5ce8d0b040693d540cb5aaf1b9fb3b "Peptostreptococcaceae"     
## 9579cc9ad7e64d3305e8aa5e53c667f7 "Ruminococcaceae"           
## be88e2bee5866989aa7c16c28646cf50 "Ruminococcaceae"           
## 059e847d26f267fa3730d112f3014b1f "Ruminococcaceae"           
## 23a5e6774a168faddfac530ac1033388 "Ruminococcaceae"           
## f2735c286490a71c359f4d5db6bdd217 "Ruminococcaceae"           
## ba0596067c4e680406c82c4baa296538 "Ruminococcaceae"           
## f2def42b08374f35a87be49c511de37a "Ruminococcaceae"           
## 8302230fee8b0e524dc372e6e97211e1 "Ruminococcaceae"           
## 8ac67871377691e5f68c2600870352ec "Ruminococcaceae"           
## 75734bf2678c55d2dbbdffa17417ab89 "Ruminococcaceae"           
## 198c7b560d46758bcbad890d07833b37 "Ruminococcaceae"           
## 75bc33d3f4be73b5221a58ddd6e73798 "Lachnospiraceae"           
## 62a7641b0fd611f2b5f56840e4afe298 "Ruminococcaceae"           
## 0c438af5dc97a32a49dc6cf46e911b17 "Veillonellaceae"           
## f414562b9ba38395a17b663355f405f8 "Lachnospiraceae"           
## f1d10bfa443393cfe67263894c84e566 "Lachnospiraceae"           
## d862ff0f8f5c9f39ae13f080aa680bb3 "Lachnospiraceae"           
## 702add448b05e3087ea6cecea7dd90b4 "Lachnospiraceae"           
## a3a479ce8ea08a480c9a96d6cd9c2f62 "Lachnospiraceae"           
## 2546dd1d30f6556190239a0f5c8efad3 "Lachnospiraceae"           
## 5891492addacafaf26c9ab65b7c17a3f "Clostridiaceae"            
## 94f2f98ac7d8d5e8ea731c9c3ee48c86 "Clostridiaceae"            
## 61880eb94d6e2c60ff0276bccb67c9ec "Christensenellaceae"       
## 0360a498b5585f9028fa802e6b4f7bf5 "Veillonellaceae"           
## 135ea3e4d147e2cf6e381bd218ca38c2 "Veillonellaceae"           
## 7be1f8896d95573e6ba7523bf6d29546 "Veillonellaceae"           
## ab7e93274f5830e83f60e578976747d3 "Veillonellaceae"           
## 5ad1971e7c113f850929b1752979a1a5 "Veillonellaceae"           
## cb9fe9ff4eb7853282a4d840335b6fc5 "Veillonellaceae"           
## d6377ab8698308388991039193fed9e6 "Erysipelotrichaceae"       
## c002515d386833fd7c4969a03a9aebb5 "Erysipelotrichaceae"       
## 99acc08c0d8bfce4ad95740ddf504a83 "Erysipelotrichaceae"       
## 51c88352cb0925e74ba66a7dd7cde265 "Erysipelotrichaceae"       
## a71a5fde3bfe18523396fab08f4e474d "Anaeroplasmataceae"        
## acaa6fe062445b95590d349c619ff73f "Erysipelotrichaceae"       
## 77be883e73ff901aea64b7487a80e245 "Erysipelotrichaceae"       
## 07ed27499a5612e2a730ef4d4a95cae9 "Erysipelotrichaceae"       
## 48ae71b68d6954a54eb355054e9ca62a "Erysipelotrichaceae"       
## eaa57f77edaae985a5784f41ece4ce33 "Streptococcaceae"          
## da3fd1a55a332ea87aa1da2b633d54b2 "Streptococcaceae"          
## a62e32c83e169200a7222bc5e937b23b "Planococcaceae"            
## bdbe4504d2313c7e46d1e5a1b4c502f3 "Staphylococcaceae"         
## 86599a57e1dcd7a14bdfd8dacbdb29c4 "Planococcaceae"            
## ff931fa606fa70b98d9cc7339959e1e4 "Planococcaceae"            
## 26d9efc3df990145f38903f8fcf86546 "Paenibacillaceae"          
## c6f61b95201848ba396fcf8f9f393bd8 "Bacillaceae"               
## 2acd7b47e3bfd5c56047c3922a32dc50 "Paenibacillaceae"          
## 56a8dc24218d559971fd66bfbc07b25e "Paenibacillaceae"          
## c8b0264dca035066a4f98e8f5f57a1fd "Paenibacillaceae"          
## 0ad56849fee2b97ca31f66083120f60a "Paenibacillaceae"          
## 0080fef6444702a9598894828d7c6480 "Sporolactobacillaceae"     
## d24f404d0e184ab79cba846971453bcd "Bacillaceae"               
## 400a504e050fa1e94dbb78a317a91676 "Aerococcaceae"             
## b5d49db9d9ccb60a34050267bfcc36fe "Aerococcaceae"             
## 2c234c87c5882dd4f414aec10fa936c2 "Enterococcaceae"           
## 0f1caf1bbdbe6b2ca659622ee70d0b63 "Carnobacteriaceae"         
## e5c43f196cbe5ab66faa3c4f467a0886 "Aerococcaceae"             
## 6b085c4046ac5ebe8ef6ac62d791bea5 "Aerococcaceae"             
## c00d929bb5c22936acc74570e3b5bdf6 "Aerococcaceae"             
## 1d05ba400871e661d4b6f5d5221ceaa0 "Aerococcaceae"             
## 4580887b2b9919823d69f37282c7eb68 "Lactobacillaceae"          
## 2e398b8d21dc0766b2cf014de5f215f9 "Lactobacillaceae"          
## babb2ebb5ca6d5b569dbcd2b4b628198 "Leuconostocaceae"          
## bf2c7a63827bc0b6e73780bd35ef1b24 "Leuconostocaceae"          
## a5d29f17bd1a64838e0d611fbcdd1ff6 "Aerococcaceae"             
## 3c7e37f4083b0b16aa9124dad86730c7 "Listeriaceae"              
## 045316716e32037c41e0b163bf4d7f21 "Acholeplasmataceae"        
## d8f53497fb4a7d7ece0196fb9f0a6ab4 "Bacteriovoracaceae"        
## 5cfcdb0adca683f26388b734166fa45b "Campylobacteraceae"        
## d372fbcdc973cce384300297bee0478f "Campylobacteraceae"        
## ae33131a40a790d5a6e096dfe63a89d8 "Helicobacteraceae"         
## 187e9220f0344b3c3fa9269ef230fc90 "Pelobacteraceae"           
## 672ee70217e3b5a9235307922a02c7f8 "Bdellovibrionaceae"        
## 5e056cc118579d9d7c95fe778b8ea768 "Cystobacteraceae"          
## 9b487aae59ee8631f146add439f853d2 "Polyangiaceae"             
## 1ae19e5736f0e1386f60a9f7c5d78fde "Polyangiaceae"             
## 0ab39039498ea9d85c86e8123448534b "Polyangiaceae"             
## 653b92284cc9d8af71788389322f0edd "Polyangiaceae"             
## e21fc8d6fb72d301fc9c60d5767cce74 "Desulfovibrionaceae"       
## e8707202237b30ae28569d165c85bf19 "Desulfomicrobiaceae"       
## f889b0623697ffab382195032c9ad941 "Desulfovibrionaceae"       
## 305ad58751bd60cdfb4c103af7c099f4 "Desulfobulbaceae"          
## 045260d3560e65d1ed7fc1184847d2ab "Nannocystaceae"            
## f31d96a0dc85b58019e54c41729a5705 "Alteromonadaceae"          
## 801ac076ebb43dd3c879924efd470f18 "Methylococcaceae"          
## 7c71dd18459d57c725a3ad9ec173d5db "Methylococcaceae"          
## 32391b052e2eb6e82b519a21b917701a "Cardiobacteriaceae"        
## 90023f83f20dc4626e11297485a2a460 "Oceanospirillaceae"        
## f79e941eee754904cdc3e35d0786a2bd "Colwelliaceae"             
## 892d322ffc17d6b4821998ef14e94580 "Oceanospirillaceae"        
## 9b44baa49a601fb4b6c50c312c901778 "Pseudomonadaceae"          
## cbb4db0a376d0da10f3409b324e572b3 "Enterobacteriaceae"        
## 2926f7065c61a289014e2ef920198e41 "Pseudomonadaceae"          
## b90f313249467f3247b2e178108f56c4 "Alteromonadaceae"          
## 9fb82f32eb82975222f78b04260eaa3a "Alteromonadaceae"          
## 23ccd8e52a41d7ca1cd3f7d18bb747b7 "Oleiphilaceae"             
## 2de364e6eaebebbbb28cca6b2ee5f322 "Halomonadaceae"            
## 100dda46eb1c9633ba33d459cad7b6d3 "Ectothiorhodospiraceae"    
## 2027d883259942129f4653bb8773ccbb "Halomonadaceae"            
## adce59f1751d627ceab8dd97f4d04c6f "Moraxellaceae"             
## 4be80be705379fe624bf4f236868c161 "Moraxellaceae"             
## 0c8e4b53a95f728aad2fb84bbd346f97 "OM60"                      
## efbb12b0a03e0073ea00bee12f98b36e "[Chromatiaceae]"           
## 1d38cdf4c8a50b1ea96f2156356de988 "Enterobacteriaceae"        
## 19a6bf2bac2f1eda36feda7b342d2fb5 "Enterobacteriaceae"        
## 27105df2940b9391e03c2d80d7f8b4f5 "Enterobacteriaceae"        
## 939aeb8878169f64a49619412a2f63b0 "Aeromonadaceae"            
## e0e1b66edfc9669ea0d9a6a802bf2788 "Vibrionaceae"              
## d89d2a592c1aca630b867e7ccb9e42a6 "Vibrionaceae"              
## 5cf7e8ff515a6a5f6104637fd70423c1 "Vibrionaceae"              
## 69a578040fb5a9fff8bc026b7909ba83 "Pseudoalteromonadaceae"    
## fbf60a3c4454aa9de8e64561fccc5345 "Alteromonadaceae"          
## a1d7db2eb229495c2c82b6983acf7e43 "Succinivibrionaceae"       
## 17fad4dc8312a2057293bfc76005b8de "Succinivibrionaceae"       
## 73dc5d7d8e076fd5a6aeddf13f9ef785 "Xanthomonadaceae"          
## 133220fc9566f8823ba6361d973f7e56 "Xanthomonadaceae"          
## 11a0aa4ba2b9f7349d89e260f7091c23 "Coxiellaceae"              
## 8a8122d28d426c268bc33a6036ee1201 "Legionellaceae"            
## 56f83521d186287a1334d08d18f63158 "Nitrosomonadaceae"         
## 8987bf7650d847a8389432b1b97b9076 "Methylophilaceae"          
## c99ed97ec81f07d7a5bf5e6d39644e78 "Rhodocyclaceae"            
## 79d01cf1a57f4ae9b2100a92fc8ccdba "Neisseriaceae"             
## 49d4b7fc67aed6a6c15b45b14ec2d0bd "Alcaligenaceae"            
## 787102493891f91105723053cb7fa472 "Oxalobacteraceae"          
## 83cfc0b49f561f34323bf84f88479fb0 "Pasteurellaceae"           
## ed4ce9dc264e70619df3ec76f6551fd6 "Pasteurellaceae"           
## ac967d4c0addb4554c76a32d34fd6c95 "Pasteurellaceae"           
## 438f1f8281a645f62d60881fd6b0fa57 "Pasteurellaceae"           
## 7fc26bb3199fb45b03be3a64086369fc "Alcaligenaceae"            
## 69c2a11ae089bcd6b89a7e0e820348a0 "Alcaligenaceae"            
## a1a04d3b99a0830ff52c65019cdbf0ae "Alcaligenaceae"            
## cb8975338b82a1cde52ea64147755a73 "Comamonadaceae"            
## cbcf57af593627cc223bc600b5fb8318 "Comamonadaceae"            
## dad64d6402e87f2685829f369810b4da "Comamonadaceae"            
## 1d4ba0b34502c3002f4e746231e00d5f "Procabacteriaceae"         
## a8f07c39cca53fb138e8007eb22aa6a1 "Neisseriaceae"             
## 94ea0cf0f0fc7c8f21b14c876a6531e5 "Neisseriaceae"             
## d689bc688fc4d75a7bb96dae07c80129 "Oxalobacteraceae"          
## 085877117ce16b29716cb7211f5bf8e0 "Sinobacteraceae"           
## 6e8ddec699ec02deed4236f0af079318 "Sinobacteraceae"           
## dc5b0a8becafb8ce2ca3326fc498464b "Moraxellaceae"             
## 1d4f2df9b6265023cd7a291fd570f21d "Moraxellaceae"             
## 9b740e8e047c98bb45cd4dc582c1a7f9 "Moraxellaceae"             
## b8a850e18c6624af91cd225fbdefa983 "Xanthomonadaceae"          
## e648c38b1b9e6300c7919c49b32f2d6f "Xanthomonadaceae"          
## c1889e2c77161500555ea720c5850b61 "Xanthomonadaceae"          
## 9b6c084f78f830b31a28de8180814ae8 "Xanthomonadaceae"          
## 88242931b35810f68ef8dd396bb1d337 "Xanthomonadaceae"          
## 3e155bea0907cecaf362cac4e87deb3d "Xanthomonadaceae"          
## 5e55605eb003f98493386574e7670725 "Xanthomonadaceae"          
## 14f6c55698300e24e20f0af01fc1362a "Syntrophaceae"             
## d59a2064644c08d1dadbbce20f19f527 "Acetobacteraceae"          
## 20e66d19c6e48da230746eb8df4fbee9 "Rhodospirillaceae"         
## db18ee1beaf8b0931f49185b7e87bb50 "Rhodospirillaceae"         
## 5bddc3e2dd40027af0348e3e496b5ede "Hyphomicrobiaceae"         
## 98c0af570beeb456ca1529e4b7539b6c "Rhizobiaceae"              
## 325c677d23378529799356c93bdbf138 "Aurantimonadaceae"         
## 184c1055f8871453d4cfb2e063826c79 "Beijerinckiaceae"          
## 8454ff06fc777ee1792f0a92c0a2a3db "Beijerinckiaceae"          
## 139b3a842bac5a67836f791535c71ed2 "Methylobacteriaceae"       
## b43b837314cfb7aef5d3c3fd8e8142b6 "Beijerinckiaceae"          
## 7eaa2034a21192be6ecfaec001f3fa08 "Caulobacteraceae"          
## c378c39c2cfe843318ac7345e6189014 "Caulobacteraceae"          
## 6669e651c7a9d2b735e9b7d496508cde "Caulobacteraceae"          
## 1a7a971d3bcf21592d1ebabf35d100fd "Caulobacteraceae"          
## dc367720df5c1ae8d78019dc83dd2e0b "Sphingomonadaceae"         
## b8f6759d312f1de655ef951649593ef0 "Sphingomonadaceae"         
## 21b486ea16b34f5b7ce3c8224c331d5e "Sphingomonadaceae"         
## ffcd590944755753b1d8ae88273c731f "Rhodospirillaceae"         
## e522565172c313a3ffddbfc619a2d21b "Rickettsiaceae"            
## d96b6207fb8725b32db97bec235ce3d0 "Rhodospirillaceae"         
## f8c6df3d56ff7649bc52d0aedbc8e048 "Acidobacteriaceae"         
## 405d0bd8bde3bbf8136655339aaffb32 "Elusimicrobiaceae"         
## 4f7b6df0faabff63004fd8e4aa84143e "Spirochaetaceae"           
## bd450cfd5b93248abf2a4b1ef4e57ae5 "Spirochaetaceae"           
## 39832721d381138daa264d1543480827 "[Borreliaceae]"            
## 8b9d573892bcf008125b830abb494242 "Nitrospiraceae"            
## 22d355b3fc4793261d21a6f9fb219f49 "Thermoanaerobacteraceae"   
## 5b34a5582c8a0efd4e8746a39925b754 "Symbiobacteriaceae"        
## 7d4cd07fe04d753bf8bcb57dc27f71b1 "Thermoactinomycetaceae"    
## 35f15070627d645a49065e8e30004ee4 "Thermoactinomycetaceae"    
## 7a282fb1eafde33e74e1af68340132cc "Thermoactinomycetaceae"    
## ba38edc1c02e03da1577a96422af5ea0 "Alicyclobacillaceae"       
## 55e81e6a020e5d9dd500a0ac51b0b283 "Ktedonobacteraceae"        
## ad02c5eee2b39f40fac1f608e9a588d2 "Anaerolinaceae"            
## fe81a158a7d2c78cdb8d494c150dab85 "Anaerolinaceae"            
## 4088b88f122d38e0d64a1691202e7ee6 "Caldilineaceae"            
## 74f297c560f6dad782d11d1b77e88621 "Chloroflexaceae"           
## 8c3abd03b35e980141bc63102af4480f "Oscillochloridaceae"       
## bf71e327691c4854a681e15b28902a68 "[Kouleothrixaceae]"        
## 8971ea6436b3f2f9d4f2f4b1bab4ad01 "Thermaceae"                
## 91d9b2a9eb8359f3b10a4ff82eaac7bb "Fibrobacteraceae"          
## 815fc729fe3c00d325ab760f6bb74b08 "Gemmatimonadaceae"         
## be014e630e00e5c6e3f0ca87daa86d1b "Coriobacteriaceae"         
## d443d45b9452b33e2f15317f488a8aff "Coriobacteriaceae"         
## 2bc3044df4d1da6e21cdc4a5aa7f2d7c "Coriobacteriaceae"         
## 1da892b315515f65dcfd83beb0e171bc "Coriobacteriaceae"         
## 84763964b516506d9a5daa198694508a "Coriobacteriaceae"         
## 4cf10e8585dbc2b18d3aa2def42863cd "Coriobacteriaceae"         
## 044575c49355d2dc1dc328d7f4cccf07 "Coriobacteriaceae"         
## 98828518c045dbd013ddf95ed960ff68 "Gaiellaceae"               
## 32b519e9b7a8e3207f070845156855a0 "Solirubrobacteraceae"      
## e9ab2e1d89fdae4700c6740323ae0d91 "Patulibacteraceae"         
## 79746a8c7e32d661ecde6164f1de5cbe "Nitriliruptoraceae"        
## c97d71471bfaf2c3e54913809ec72f2a "Propionibacteriaceae"      
## 9d2d8b251de60fe5dff92e5e0b4ed3f7 "Streptomycetaceae"         
## 468b178baa29eebee837710342a0f910 "Nocardioidaceae"           
## 49ce92d31439808d0d1bea75a00d5bfc "Nocardioidaceae"           
## 537d15ab7624090dc5c79090bd6a167e "Propionibacteriaceae"      
## 6a817ad430bbcadd29c75840b4fd25c4 "Nocardioidaceae"           
## 0a8448ddb119a2aa1e0ae86928097f91 "Frankiaceae"               
## 62058d158b24b3fbea81b2be7061d67d "Pseudonocardiaceae"        
## f80f713bc2c318c2d2e857fa60324f71 "Actinomycetaceae"          
## fb96448a13cbd1b35b97f5ea7c9d9f0c "Actinomycetaceae"          
## 492710d4b2c77ae8a3887b6b67edf135 "Nocardiopsaceae"           
## 399b720f381d18fb6054810664faf3b1 "Nakamurellaceae"           
## 4e624224b836599c23297d3c0d738f2c "Nakamurellaceae"           
## fe1f9c1511f40357b7ff3f062a9e9a2f "Nakamurellaceae"           
## db89f0083e3043374e273f1168399165 "Micromonosporaceae"        
## 9606f5b31c4365a210f062af56429ba4 "Micromonosporaceae"        
## cf624c989019ccb39a8316fd82969fca "Micromonosporaceae"        
## 78bb7782ad610368d38621de127fa83c "Micromonosporaceae"        
## 7a4040c73abc580073bdb4eb1d74a33d "Cryptosporangiaceae"       
## a63e98d52785ca8e8af60d0804af5dae "Mycobacteriaceae"          
## eb07445c23ec6a0baaf838fec7f3f2a5 "Dietziaceae"               
## ef289d460d88b8bf99288c9ccafa3de4 "Nocardiaceae"              
## d982cb2e9c52d04a131bfd6bfd57143f "Geodermatophilaceae"       
## f10abcfb58070db144ab557203b15112 "Geodermatophilaceae"       
## 2e3e409911947f6b58055dac76eafff2 "Bifidobacteriaceae"        
## 6a8e34c34c852052fbb2ef47f31923cf "Bifidobacteriaceae"        
## 69b20ec4a1f82d5d7bfccce73e181144 "Bifidobacteriaceae"        
## 2f3464d9017dbcc3c07539e9e6d031d1 "Micrococcaceae"            
## 19b23b503d10795479f12bed782e37bf "Dermabacteraceae"          
## 13c1dc3da2ab678bb67e738463291f41 "Intrasporangiaceae"        
## 0f7c178d133e189017d861892caf1b54 "Intrasporangiaceae"        
## 0c416bb1ef62f13288e440253605f1f6 "Brevibacteriaceae"         
## a9ea27c012d71729be0af434b0135b8f "Kineosporiaceae"           
## 9910430d69cf086a7a32730d88e36ca1 "Kineosporiaceae"           
## bc5dc688aca3e85050859ccffb837227 "Actinomycetaceae"          
## 6cfcb015a00c6f3fb16e6eec63f4a35c "Micrococcaceae"            
## 1034ce7814ed4bb5c4506bc6b75eaa3f "Micrococcaceae"            
## 9dc76e20f768b3449b07c21ff7377623 "Microbacteriaceae"         
## 4353875d14dabd7fe11946d21ac50b66 "Microbacteriaceae"         
## 1c927fead59f669c939d603634ce60e3 "Microbacteriaceae"         
## cc06b4a0146591e922e1f9c019a63485 "Microbacteriaceae"         
## c2b4b05dc7cde089c596aaaea2349b57 "ACK-M1"                    
## c0fcac392fda5b2c85f7eff24b4a08ed "Gordoniaceae"              
## fdc1a7c3ebe3c43c9205147181cadf6b "Corynebacteriaceae"        
## e229fd918de8f64d13ec2a69bab94a5d "Thermomonosporaceae"       
## af0d699336503dd28940bf80973df0d1 "Thermomonosporaceae"       
## 7beb6afb10d4a33729f38eae58eb86fe "C111"                      
## 9f213cf8c7852cace5c0bae0997ca479 "Iamiaceae"                 
## e5516025a4d9f48a9fd7248989289b17 "Xenococcaceae"             
## 265b94ca9e486aa0e39696dbf1004bab "Pseudanabaenaceae"         
## fc5a4fb7042e9842c36f36e0ab934610 "Chroococcaceae"            
## c11850f778c3ed2aad77e905a962df9f "Xenococcaceae"             
## e1defeafac8215315915a82ed015dcb2 "Nostocaceae"               
## 4b4b20eeb4a4ccbd441b8d2ef9f31bf7 "Nostocaceae"               
## 5575e3a3b9446bc439d3a13064c07e21 "Nostocaceae"               
## 565f359611711ce61076b0f3f8eb9453 "Nostocaceae"               
## 83196c5429def72c900061a0a8c5b49b "Scytonemataceae"           
## 0c6f8e3cb66947204cae236072a04a74 "Phormidiaceae"             
## 2472bec6d09ab949b643cb1a4f41816b "Pseudanabaenaceae"         
## de5d66672c644945370a3bd62bd2caf4 "Pseudanabaenaceae"         
## 03ca951e561969caf45da606fde67866 "Trebouxiophyceae"          
## d02aa15268aade892ad5dff83af3e7da "Trebouxiophyceae"          
## 3cd6ab4607d7c365dfdc11a48bf893c5 "Phormidiaceae"             
## 48b2489d2a8ef650129b144899cdf302 "Chlamydomonadaceae"        
## 0040892ff482919cb88018e43a333cca "Chlamydomonadaceae"        
## a0051aa570b907944f08a912f8bc09fd "Ulvophyceae"               
## d49b641988fea3844b9de1e6ad26ee98 "Hyphomicrobiaceae"         
## 14e8f8943c5595bbea2cca1cc3c383d0 "Holophagaceae"             
## d9b514bc64139095efef65a654a1d0e2 "Holophagaceae"             
## f54c0eca0d64aade6c60bbad968da659 "FW"                        
## 39e9884255a81dfa04b47a2b11e3ef5b "Phycisphaeraceae"          
## aa33408e38ea9b07aa856e8e6701b0da "Acidobacteriaceae"         
## cf7bf8f703a8335c0d3018f4604f1cb6 "Opitutaceae"               
## 31f232781685558bf9d62e35e8f237f9 "Verrucomicrobiaceae"       
## b8b9f753c83c855cc38aff497e5e89ce "[Chthoniobacteraceae]"     
## 85e29914e803ab4d6fb6602bd6b9ff00 "[Chthoniobacteraceae]"     
## d37b60c688fcca90997aadce4c64d5a9 "[Pedosphaeraceae]"         
## 107aca9889569069069d195bd8a31697 "[Chthoniobacteraceae]"     
## bd3849fc9106f9cdacb9341795c8cb29 "[Chthoniobacteraceae]"     
## b5d0c6f1b9e8a8302389f77b79dcda85 "[Chthoniobacteraceae]"     
## bd1b5b2bb3a3f6cd721255c7a706da1c "Verrucomicrobiaceae"       
## b9bad8448867f57e6a14c1a242c48774 "Verrucomicrobiaceae"       
## b22df4733817d748ec348e7f3e6b33eb "Verrucomicrobiaceae"       
## 8941145147965d89bfcc4e88c0b9535b "[Chthoniobacteraceae]"     
## 0d9178b0087a618145122137d5f02c9d "Thermoanaerobacteraceae"   
## 1d44015ea379303fcf6b84e6de3b56fe "Isosphaeraceae"            
## abbfa75d6cee07b5d473575e6fc31ca6 "Rhabdochlamydiaceae"       
## ebf9bf8eb6025551e0c72b979eadee03 "Simkaniaceae"              
## 46d7cb3e670b0a7c6be9f9e87b8a9062 "Parachlamydiaceae"         
## 77ade2a27cd5cf184bc7c566b5e40350 "Dethiosulfovibrionaceae"   
## a0cdbcafbb2e9ca1d27ec77bf2e8d58d "Synergistaceae"            
## a79f2d2819aa6abbb25c3d52f0a6d88e "Deferribacteraceae"        
## 9640db4284f6de2f96bc6a089999e1d9 "Leptospiraceae"            
##                                  Genus                          Species
## 738f9b43067c64d7dd19a58e16776ca1 "vadinCA11"                    NA     
## bf3ea7575ee681f6cc071fc10a9b0c9e "Methanosphaera"               NA     
## 81ca8fa4a795e9929b18c343fa7e5d6d "Methanobrevibacter"           NA     
## fce80713066a40d6d40c78a2bfc701f0 "u114"                         NA     
## da2d307acbc750e709821f37106a97ee "Sneathia"                     NA     
## ec4dafd949562cb1c67abf1edb908e45 "Streptobacillus"              NA     
## 937486517cc80db8a7247c8d9cedcb6c "Leptotrichia"                 NA     
## 2960c4868268ab63fffd54d389e709f4 "Mycoplasma"                   NA     
## b1cc0afab8aabe335f3d2183a8f862a8 "Truepera"                     NA     
## d812033144facb838340db156bc7cddb "B-42"                         NA     
## a8d5e516d55e0f840a901a1754faf215 "Deinobacterium"               NA     
## b3f7ce9240052a0925ec9e675b5c5801 "Deinococcus"                  NA     
## dd2c236c7e7f2b0eca6a81e2ac82e5e9 "CM44"                         NA     
## f572830d714e07d0b571ccb4029c577b "R18-435"                      NA     
## 12c129f217c4ceeb3f4e6992749ee828 "Fimbriimonas"                 NA     
## 1ef109986a98fbad2514a0bdde298328 "Odoribacter"                  NA     
## 550a6c75a980e53ebe63fb821d692cf3 "Parasegitibacter"             NA     
## 08790daac50cd048ed5839225585e108 "Filimonas"                    NA     
## 9cbea8ff52e16e14d63f27d5f6f9ee70 "Ferruginibacter"              NA     
## 38876d2e7234ac8c535d914e1b89c7f2 "Terrimonas"                   NA     
## 937da713490e1d08e8727822deaeb6ca "Trachelomonas"                NA     
## 32756a7fcc03fdddee0c5b2da35b7940 "Solitalea"                    NA     
## 6ba1a63b03ed1667ddedc0813b737f0d "Alistipes"                    NA     
## 23f0414ba47f7c7999f913671268837d "Rikenella"                    NA     
## 5ada85d7be5d55db0cd492bca13b3003 "Cytophaga"                    NA     
## a51c11ce94e4c3cedeeeb25ccda839bb "Bacteroides"                  NA     
## 183f2ec8041f54e28b279213dab7f242 "Paraprevotella"               NA     
## 3ec9a72eea2934c7e20bf5e3840b3935 "Macellibacteroides"           NA     
## 6549baa73149f7a4de583300732198e3 "Porphyromonas"                NA     
## f4871a37ef764e383f723e547ad345d3 "Petrimonas"                   NA     
## 12332a0b15374a26f88d178f33975164 "Barnesiella"                  NA     
## 6fa2a60e9fa2afc9bb356bff76e8aea7 "Lishizhenia"                  NA     
## 7ef9ec92fa1dc4d4b175a2590b38c1e3 "Coccinistipes"                NA     
## 9d0ce3ffd40f17516f311a4f01ce71c3 "Mucilaginibacter"             NA     
## 23ebb02f88264051fb546154a4b76f1f "Pedobacter"                   NA     
## 2c2e6c9719c3d353fc8fc4c29277bf3a "Sphingobacterium"             NA     
## e93b056509933455a642b22131e787f6 "Tenacibaculum"                NA     
## 2f4128d15aa3f31e65bb6be743cf2652 "Flexibacter"                  NA     
## 82a38739a3d57c68d7488b32235fd9c8 "Persicivirga"                 NA     
## e87605af38d7adbc36e9bf2ccb4b9ed1 "Flavobacterium"               NA     
## 675f216a655188ee527413d79502e884 "Nonlabens"                    NA     
## fd67289a69cb1b8b911c9c0d5aae561c "Myroides"                     NA     
## 0156833a719406d6720169fa7c1a8c4f "Pseudozobellia"               NA     
## 394637d50ed3fa18f7ad4e5f459950bf "Yeosuana"                     NA     
## 727cd1eebae3ae24468583a5fd29bf40 "Zhouia"                       NA     
## fe148c0776bd59b90cb0a4d2f18a7431 "Capnocytophaga"               NA     
## 87b5fc5e91a8d3cc174f4741e97756eb "Weeksella"                    NA     
## 97904005472b49b5a729b1f7470c3bce "Elizabethkingia"              NA     
## 0d1d623d430214d67ab7dd50d86923eb "Bergeyella"                   NA     
## e0534df6ab1aeb8c188f3b0768b7d5ed "Ornithobacterium"             NA     
## 7f356ca83a2db14690a64a74ef25a18a "5-7N15"                       NA     
## a88bc39d28216b7fea5c260c1eba645b "CF231"                        NA     
## df0e399449afea146ca01aff07d5422e "[Prevotella]"                 NA     
## 3abf10c0fb708bc94c3ea4dd299e0970 "Prevotella"                   NA     
## 22ec7a68d4ffe650f8dd1151196824ae "YRC22"                        NA     
## 4431ece8c33501e69a7108763af73b9a "Cytophaga"                    NA     
## 943f60dee4de6bf45e42e9305d688b0c "Emticicia"                    NA     
## 2295bf9acbfa418fbcd3b30754f6148e "Leadbetterella"               NA     
## 0a8e379dd40b23d151f6392ed1a51934 "Cesiribacter"                 NA     
## 4ac7304960d351f3fde8c6b271e02cd1 "Rhodocytophaga"               NA     
## 74156312fe86d82180dcebd7fa2f1d3b "Marinoscillum"                NA     
## a6c1c1db83cc085b6f4410843de68aec "Marivirga"                    NA     
## abd4e33c5a5b25b15f743da0ba2d47de "Porifericola"                 NA     
## 88063ce6d940ae9490d8f68ebbe70efd "Rhodonellum"                  NA     
## 76750ffa90fdd5952e8570f9a1fc11f9 "Echinicola"                   NA     
## 0d81c4844619813dd873a65bcf91b75b "Indibacter"                   NA     
## 87ae24a9562a267c0c47df8e04a60f89 "Algoriphagus"                 NA     
## 5e75d3a55ceb4dc7a55910426de76734 "Siphonobacter"                NA     
## c99b81e959d197f32acce3adc9c4fab5 "Flectobacillus"               NA     
## 4c16e214394f648bcce3b069ef859388 "Dyadobacter"                  NA     
## bde4c36da80878e658df02d338931982 "Rudanella"                    NA     
## 61899b1d726126ee51b7335a9e17ea3f "Larkinella"                   NA     
## d2585e354502d89dc5e0a6e923551ec4 "Spirosoma"                    NA     
## c5a6d0e5a5aec5fb2aeaea82dea15305 "Rubricoccus"                  NA     
## 46546f341eac9b2125a8e152eef86d82 "Asteroleplasma"               NA     
## f39b347d2f6c66682fd9982cae666e88 "Succinispira"                 NA     
## 9dbb7cbacf6d05c6f914fd172280c3ff "Acidaminococcus"              NA     
## 8f9ad93911aa5eaeb33b21f8f7c2c45f "Anaerofustis"                 NA     
## d27c33a2c70998d3ea63eb1ff3cb0221 "rc4-4"                        NA     
## d5167fdceb8a3baf484e932653cce66b "Peptococcus"                  NA     
## 92591f68fc9a379243ba99075a0c1a11 "Halocella"                    NA     
## 7b0402e21e2605b6efc8f9ee96439660 "Sporanaerobacter"             NA     
## 108ec75ebd3d17a56bfabec9ab334e0e "WAL_1855D"                    NA     
## 49e2fbc314555e9fd5f1accf0fb91af8 "1-68"                         NA     
## f3f29b983fe8c0dfe37668e9d4ae8bc6 "Gallicola"                    NA     
## 569418df588c6249c6525811063aacf5 "Finegoldia"                   NA     
## 65a75861ea5af532e70ba307bf70a9a9 "Parvimonas"                   NA     
## bb3291ec469409c1d58c5b0fdc933ec6 "Haloplasma"                   NA     
## ee9bbcdf5eab5edd0596f444214183cc "Peptoniphilus"                NA     
## 90fe5379a170a7caa71f8f383f485f2b "Helcococcus"                  NA     
## 0e7f78e494e734305ea59cd0caafa1b8 "Filifactor"                   NA     
## 95b83723ec29f8943be9bb7d717c5a4b "Peptostreptococcus"           NA     
## 257742c10ede9357a9f59a3217461ae5 "Proteocatella"                NA     
## 1db331ef1773d7b27b8e386278202b7e "[Clostridium]"                NA     
## dd5ce8d0b040693d540cb5aaf1b9fb3b "Clostridium"                  NA     
## 9579cc9ad7e64d3305e8aa5e53c667f7 "Sporobacter"                  NA     
## be88e2bee5866989aa7c16c28646cf50 "Oscillospira"                 NA     
## 059e847d26f267fa3730d112f3014b1f "Butyricicoccus"               NA     
## 23a5e6774a168faddfac530ac1033388 "Ethanoligenens"               NA     
## f2735c286490a71c359f4d5db6bdd217 "Gemmiger"                     NA     
## ba0596067c4e680406c82c4baa296538 "Subdoligranulum"              NA     
## f2def42b08374f35a87be49c511de37a "Faecalibacterium"             NA     
## 8302230fee8b0e524dc372e6e97211e1 "Anaerotruncus"                NA     
## 8ac67871377691e5f68c2600870352ec "Clostridium"                  NA     
## 75734bf2678c55d2dbbdffa17417ab89 "Ruminococcus"                 NA     
## 198c7b560d46758bcbad890d07833b37 "Bacteroides"                  NA     
## 75bc33d3f4be73b5221a58ddd6e73798 "Dorea"                        NA     
## 62a7641b0fd611f2b5f56840e4afe298 "Papillibacter"                NA     
## 0c438af5dc97a32a49dc6cf46e911b17 "Propionispora"                NA     
## f414562b9ba38395a17b663355f405f8 "Ruminococcus"                 NA     
## f1d10bfa443393cfe67263894c84e566 "Lactonifactor"                NA     
## d862ff0f8f5c9f39ae13f080aa680bb3 "Roseburia"                    NA     
## 702add448b05e3087ea6cecea7dd90b4 "Coprococcus"                  NA     
## a3a479ce8ea08a480c9a96d6cd9c2f62 "Clostridium"                  NA     
## 2546dd1d30f6556190239a0f5c8efad3 "Defluviitalea"                NA     
## 5891492addacafaf26c9ab65b7c17a3f "Clostridium"                  NA     
## 94f2f98ac7d8d5e8ea731c9c3ee48c86 "Candidatus Arthromitus"       NA     
## 61880eb94d6e2c60ff0276bccb67c9ec "Christensenella"              NA     
## 0360a498b5585f9028fa802e6b4f7bf5 "Dialister"                    NA     
## 135ea3e4d147e2cf6e381bd218ca38c2 "Anaerosinus"                  NA     
## 7be1f8896d95573e6ba7523bf6d29546 "Selenomonas"                  NA     
## ab7e93274f5830e83f60e578976747d3 "Megasphaera"                  NA     
## 5ad1971e7c113f850929b1752979a1a5 "Mitsuokella"                  NA     
## cb9fe9ff4eb7853282a4d840335b6fc5 "Megamonas"                    NA     
## d6377ab8698308388991039193fed9e6 "gut"                          NA     
## c002515d386833fd7c4969a03a9aebb5 "Asteroleplasma"               NA     
## 99acc08c0d8bfce4ad95740ddf504a83 "Clostridium"                  NA     
## 51c88352cb0925e74ba66a7dd7cde265 "Catenibacterium"              NA     
## a71a5fde3bfe18523396fab08f4e474d "gut"                          NA     
## acaa6fe062445b95590d349c619ff73f "[Eubacterium]"                NA     
## 77be883e73ff901aea64b7487a80e245 "Bulleidia"                    NA     
## 07ed27499a5612e2a730ef4d4a95cae9 "Holdemania"                   NA     
## 48ae71b68d6954a54eb355054e9ca62a "Anaerorhabdus"                NA     
## eaa57f77edaae985a5784f41ece4ce33 "Lactococcus"                  NA     
## da3fd1a55a332ea87aa1da2b633d54b2 "Streptococcus"                NA     
## a62e32c83e169200a7222bc5e937b23b "Staphylococcus"               NA     
## bdbe4504d2313c7e46d1e5a1b4c502f3 "Macrococcus"                  NA     
## 86599a57e1dcd7a14bdfd8dacbdb29c4 "Sporosarcina"                 NA     
## ff931fa606fa70b98d9cc7339959e1e4 "Kurthia"                      NA     
## 26d9efc3df990145f38903f8fcf86546 "Brevibacillus"                NA     
## c6f61b95201848ba396fcf8f9f393bd8 "Bacillus"                     NA     
## 2acd7b47e3bfd5c56047c3922a32dc50 "Aneurinibacillus"             NA     
## 56a8dc24218d559971fd66bfbc07b25e "Paenibacillus"                NA     
## c8b0264dca035066a4f98e8f5f57a1fd "Saccharibacillus"             NA     
## 0ad56849fee2b97ca31f66083120f60a "Ammoniphilus"                 NA     
## 0080fef6444702a9598894828d7c6480 "Tuberibacillus"               NA     
## d24f404d0e184ab79cba846971453bcd "Sinobaca"                     NA     
## 400a504e050fa1e94dbb78a317a91676 "Lacticigenium"                NA     
## b5d49db9d9ccb60a34050267bfcc36fe "Granulicatella"               NA     
## 2c234c87c5882dd4f414aec10fa936c2 "Enterococcus"                 NA     
## 0f1caf1bbdbe6b2ca659622ee70d0b63 "Isobaculum"                   NA     
## e5c43f196cbe5ab66faa3c4f467a0886 "Marinilactibacillus"          NA     
## 6b085c4046ac5ebe8ef6ac62d791bea5 "Alkalibacterium"              NA     
## c00d929bb5c22936acc74570e3b5bdf6 "Atopostipes"                  NA     
## 1d05ba400871e661d4b6f5d5221ceaa0 "Atopococcus"                  NA     
## 4580887b2b9919823d69f37282c7eb68 "Pediococcus"                  NA     
## 2e398b8d21dc0766b2cf014de5f215f9 "Lactobacillus"                NA     
## babb2ebb5ca6d5b569dbcd2b4b628198 "Weissella"                    NA     
## bf2c7a63827bc0b6e73780bd35ef1b24 "Leuconostoc"                  NA     
## a5d29f17bd1a64838e0d611fbcdd1ff6 "Abiotrophia"                  NA     
## 3c7e37f4083b0b16aa9124dad86730c7 "Brochothrix"                  NA     
## 045316716e32037c41e0b163bf4d7f21 "Acholeplasma"                 NA     
## d8f53497fb4a7d7ece0196fb9f0a6ab4 "Peredibacter"                 NA     
## 5cfcdb0adca683f26388b734166fa45b "Arcobacter"                   NA     
## d372fbcdc973cce384300297bee0478f "Campylobacter"                NA     
## ae33131a40a790d5a6e096dfe63a89d8 "Helicobacter"                 NA     
## 187e9220f0344b3c3fa9269ef230fc90 "Desulfuromonas"               NA     
## 672ee70217e3b5a9235307922a02c7f8 "Bdellovibrio"                 NA     
## 5e056cc118579d9d7c95fe778b8ea768 "Cystobacter"                  NA     
## 9b487aae59ee8631f146add439f853d2 "Phaselicystis"                NA     
## 1ae19e5736f0e1386f60a9f7c5d78fde "Aetherobacter"                NA     
## 0ab39039498ea9d85c86e8123448534b "Byssovorax"                   NA     
## 653b92284cc9d8af71788389322f0edd "Polyangium"                   NA     
## e21fc8d6fb72d301fc9c60d5767cce74 "Bilophila"                    NA     
## e8707202237b30ae28569d165c85bf19 "Desulfomicrobium"             NA     
## f889b0623697ffab382195032c9ad941 "Desulfovibrio"                NA     
## 305ad58751bd60cdfb4c103af7c099f4 "Desulfocapsa"                 NA     
## 045260d3560e65d1ed7fc1184847d2ab "Nannocystis"                  NA     
## f31d96a0dc85b58019e54c41729a5705 "Simiduia"                     NA     
## 801ac076ebb43dd3c879924efd470f18 "Methylobacter"                NA     
## 7c71dd18459d57c725a3ad9ec173d5db "Methylosarcina"               NA     
## 32391b052e2eb6e82b519a21b917701a "Suttonella"                   NA     
## 90023f83f20dc4626e11297485a2a460 "Oceanospirillum"              NA     
## f79e941eee754904cdc3e35d0786a2bd "Thalassomonas"                NA     
## 892d322ffc17d6b4821998ef14e94580 "Neptunomonas"                 NA     
## 9b44baa49a601fb4b6c50c312c901778 "Pseudomonas"                  NA     
## cbb4db0a376d0da10f3409b324e572b3 "Pseudomonas"                  NA     
## 2926f7065c61a289014e2ef920198e41 "Serpens"                      NA     
## b90f313249467f3247b2e178108f56c4 "Gilvimarinus"                 NA     
## 9fb82f32eb82975222f78b04260eaa3a "Cellvibrio"                   NA     
## 23ccd8e52a41d7ca1cd3f7d18bb747b7 "Oleiphilus"                   NA     
## 2de364e6eaebebbbb28cca6b2ee5f322 "Halomonas"                    NA     
## 100dda46eb1c9633ba33d459cad7b6d3 "Thioalkalivibrio"             NA     
## 2027d883259942129f4653bb8773ccbb "Haererehalobacter"            NA     
## adce59f1751d627ceab8dd97f4d04c6f "Alkanindiges"                 NA     
## 4be80be705379fe624bf4f236868c161 "Acinetobacter"                NA     
## 0c8e4b53a95f728aad2fb84bbd346f97 "Haliea"                       NA     
## efbb12b0a03e0073ea00bee12f98b36e "Rheinheimera"                 NA     
## 1d38cdf4c8a50b1ea96f2156356de988 "Pantoea"                      NA     
## 19a6bf2bac2f1eda36feda7b342d2fb5 "Proteus"                      NA     
## 27105df2940b9391e03c2d80d7f8b4f5 "Brenneria"                    NA     
## 939aeb8878169f64a49619412a2f63b0 "Aeromonas"                    NA     
## e0e1b66edfc9669ea0d9a6a802bf2788 "Listonella"                   NA     
## d89d2a592c1aca630b867e7ccb9e42a6 "Vibrio"                       NA     
## 5cf7e8ff515a6a5f6104637fd70423c1 "Enterovibrio"                 NA     
## 69a578040fb5a9fff8bc026b7909ba83 "Pseudoalteromonas"            NA     
## fbf60a3c4454aa9de8e64561fccc5345 "Alteromonas"                  NA     
## a1d7db2eb229495c2c82b6983acf7e43 "Succinivibrio"                NA     
## 17fad4dc8312a2057293bfc76005b8de "Anaerobiospirillum"           NA     
## 73dc5d7d8e076fd5a6aeddf13f9ef785 "Wohlfahrtiimonas"             NA     
## 133220fc9566f8823ba6361d973f7e56 "Ignatzschineria"              NA     
## 11a0aa4ba2b9f7349d89e260f7091c23 "Rickettsiella"                NA     
## 8a8122d28d426c268bc33a6036ee1201 "Legionella"                   NA     
## 56f83521d186287a1334d08d18f63158 "Nitrosospira"                 NA     
## 8987bf7650d847a8389432b1b97b9076 "Methylotenera"                NA     
## c99ed97ec81f07d7a5bf5e6d39644e78 "Azospira"                     NA     
## 79d01cf1a57f4ae9b2100a92fc8ccdba "Iodobacter"                   NA     
## 49d4b7fc67aed6a6c15b45b14ec2d0bd "Bordetella"                   NA     
## 787102493891f91105723053cb7fa472 "Massilia"                     NA     
## 83cfc0b49f561f34323bf84f88479fb0 "Pasteurella"                  NA     
## ed4ce9dc264e70619df3ec76f6551fd6 "Nicoletella"                  NA     
## ac967d4c0addb4554c76a32d34fd6c95 "Bibersteinia"                 NA     
## 438f1f8281a645f62d60881fd6b0fa57 "Actinobacillus"               NA     
## 7fc26bb3199fb45b03be3a64086369fc "Pigmentiphaga"                NA     
## 69c2a11ae089bcd6b89a7e0e820348a0 "Kerstersia"                   NA     
## a1a04d3b99a0830ff52c65019cdbf0ae "Achromobacter"                NA     
## cb8975338b82a1cde52ea64147755a73 "Acidovorax"                   NA     
## cbcf57af593627cc223bc600b5fb8318 "Sphaerotilus"                 NA     
## dad64d6402e87f2685829f369810b4da "Limnobacter"                  NA     
## 1d4ba0b34502c3002f4e746231e00d5f "Procabacter"                  NA     
## a8f07c39cca53fb138e8007eb22aa6a1 "Kingella"                     NA     
## 94ea0cf0f0fc7c8f21b14c876a6531e5 "Neisseria"                    NA     
## d689bc688fc4d75a7bb96dae07c80129 "Pseudoburkholderia"           NA     
## 085877117ce16b29716cb7211f5bf8e0 "Sinobacter"                   NA     
## 6e8ddec699ec02deed4236f0af079318 "Alkanibacter"                 NA     
## dc5b0a8becafb8ce2ca3326fc498464b "Psychrobacter"                NA     
## 1d4f2df9b6265023cd7a291fd570f21d "Moraxella"                    NA     
## 9b740e8e047c98bb45cd4dc582c1a7f9 "Enhydrobacter"                NA     
## b8a850e18c6624af91cd225fbdefa983 "Fulvimonas"                   NA     
## e648c38b1b9e6300c7919c49b32f2d6f "Rhodanobacter"                NA     
## c1889e2c77161500555ea720c5850b61 "Aquimonas"                    NA     
## 9b6c084f78f830b31a28de8180814ae8 "Lysobacter"                   NA     
## 88242931b35810f68ef8dd396bb1d337 "Thermomonas"                  NA     
## 3e155bea0907cecaf362cac4e87deb3d "Achromobacter"                NA     
## 5e55605eb003f98493386574e7670725 "Pseudoxanthomonas"            NA     
## 14f6c55698300e24e20f0af01fc1362a "Syntrophus"                   NA     
## d59a2064644c08d1dadbbce20f19f527 "Roseomonas"                   NA     
## 20e66d19c6e48da230746eb8df4fbee9 "Skermanella"                  NA     
## db18ee1beaf8b0931f49185b7e87bb50 "Defluviicoccus"               NA     
## 5bddc3e2dd40027af0348e3e496b5ede "Rhodomicrobium"               NA     
## 98c0af570beeb456ca1529e4b7539b6c "Rhizobium"                    NA     
## 325c677d23378529799356c93bdbf138 "Aurantimonas"                 NA     
## 184c1055f8871453d4cfb2e063826c79 "Methylocapsa"                 NA     
## 8454ff06fc777ee1792f0a92c0a2a3db "Salinarimonas"                NA     
## 139b3a842bac5a67836f791535c71ed2 "Methylobacterium"             NA     
## b43b837314cfb7aef5d3c3fd8e8142b6 "Chelatococcus"                NA     
## 7eaa2034a21192be6ecfaec001f3fa08 "Caulobacter"                  NA     
## c378c39c2cfe843318ac7345e6189014 "Nitrobacteria"                NA     
## 6669e651c7a9d2b735e9b7d496508cde "Asticcacaulis"                NA     
## 1a7a971d3bcf21592d1ebabf35d100fd "Brevundimonas"                NA     
## dc367720df5c1ae8d78019dc83dd2e0b "Sphingosinicella"             NA     
## b8f6759d312f1de655ef951649593ef0 "Sphingomonas"                 NA     
## 21b486ea16b34f5b7ce3c8224c331d5e "Novosphingobium"              NA     
## ffcd590944755753b1d8ae88273c731f "magnetite-containing"         NA     
## e522565172c313a3ffddbfc619a2d21b "Wolbachia"                    NA     
## d96b6207fb8725b32db97bec235ce3d0 "Reyranella"                   NA     
## f8c6df3d56ff7649bc52d0aedbc8e048 "Acidopila"                    NA     
## 405d0bd8bde3bbf8136655339aaffb32 "Elusimicrobium"               NA     
## 4f7b6df0faabff63004fd8e4aa84143e "Treponema"                    NA     
## bd450cfd5b93248abf2a4b1ef4e57ae5 "Spirochaeta"                  NA     
## 39832721d381138daa264d1543480827 "Spironema"                    NA     
## 8b9d573892bcf008125b830abb494242 "Nitrospira"                   NA     
## 22d355b3fc4793261d21a6f9fb219f49 "Ammonifex"                    NA     
## 5b34a5582c8a0efd4e8746a39925b754 "Symbiobacterium"              NA     
## 7d4cd07fe04d753bf8bcb57dc27f71b1 "Planifilum"                   NA     
## 35f15070627d645a49065e8e30004ee4 "Laceyella"                    NA     
## 7a282fb1eafde33e74e1af68340132cc "Thermoactinomyces"            NA     
## ba38edc1c02e03da1577a96422af5ea0 "Alicyclobacillus"             NA     
## 55e81e6a020e5d9dd500a0ac51b0b283 "Ktedonobacter"                NA     
## ad02c5eee2b39f40fac1f608e9a588d2 "Leptolinea"                   NA     
## fe81a158a7d2c78cdb8d494c150dab85 "Anaerolinea"                  NA     
## 4088b88f122d38e0d64a1691202e7ee6 "Litorilinea"                  NA     
## 74f297c560f6dad782d11d1b77e88621 "Chloronema"                   NA     
## 8c3abd03b35e980141bc63102af4480f "Oscillochloris"               NA     
## bf71e327691c4854a681e15b28902a68 "Kouleothrix"                  NA     
## 8971ea6436b3f2f9d4f2f4b1bab4ad01 "Thermus"                      NA     
## 91d9b2a9eb8359f3b10a4ff82eaac7bb "Fibrobacter"                  NA     
## 815fc729fe3c00d325ab760f6bb74b08 "Gemmatimonas"                 NA     
## be014e630e00e5c6e3f0ca87daa86d1b "Atopobium"                    NA     
## d443d45b9452b33e2f15317f488a8aff "Collinsella"                  NA     
## 2bc3044df4d1da6e21cdc4a5aa7f2d7c "Eggerthella"                  NA     
## 1da892b315515f65dcfd83beb0e171bc "Paraeggerthella"              NA     
## 84763964b516506d9a5daa198694508a "Enterococcus"                 NA     
## 4cf10e8585dbc2b18d3aa2def42863cd "Slackia"                      NA     
## 044575c49355d2dc1dc328d7f4cccf07 "Olsenella"                    NA     
## 98828518c045dbd013ddf95ed960ff68 "Gaiella"                      NA     
## 32b519e9b7a8e3207f070845156855a0 "Solirubrobacter"              NA     
## e9ab2e1d89fdae4700c6740323ae0d91 "Patulibacter"                 NA     
## 79746a8c7e32d661ecde6164f1de5cbe "Nitriliruptor"                NA     
## c97d71471bfaf2c3e54913809ec72f2a "Brooklawnia"                  NA     
## 9d2d8b251de60fe5dff92e5e0b4ed3f7 "Streptomyces"                 NA     
## 468b178baa29eebee837710342a0f910 "Nocardioides"                 NA     
## 49ce92d31439808d0d1bea75a00d5bfc "Kribbella"                    NA     
## 537d15ab7624090dc5c79090bd6a167e "Microlunatus"                 NA     
## 6a817ad430bbcadd29c75840b4fd25c4 "Marmoricola"                  NA     
## 0a8448ddb119a2aa1e0ae86928097f91 "Kaistibacter"                 NA     
## 62058d158b24b3fbea81b2be7061d67d "Actinomycetospora"            NA     
## f80f713bc2c318c2d2e857fa60324f71 "Varibaculum"                  NA     
## fb96448a13cbd1b35b97f5ea7c9d9f0c "Actinomyces"                  NA     
## 492710d4b2c77ae8a3887b6b67edf135 "Nocardiopsis"                 NA     
## 399b720f381d18fb6054810664faf3b1 "Nakamurella"                  NA     
## 4e624224b836599c23297d3c0d738f2c "Saxeibacter"                  NA     
## fe1f9c1511f40357b7ff3f062a9e9a2f "Humicoccus"                   NA     
## db89f0083e3043374e273f1168399165 "Catenuloplanes"               NA     
## 9606f5b31c4365a210f062af56429ba4 "Micromonospora"               NA     
## cf624c989019ccb39a8316fd82969fca "Rugosimonospora"              NA     
## 78bb7782ad610368d38621de127fa83c "Actinoplanes"                 NA     
## 7a4040c73abc580073bdb4eb1d74a33d "Cryptosporangium"             NA     
## a63e98d52785ca8e8af60d0804af5dae "Mycobacterium"                NA     
## eb07445c23ec6a0baaf838fec7f3f2a5 "Dietzia"                      NA     
## ef289d460d88b8bf99288c9ccafa3de4 "Rhodococcus"                  NA     
## d982cb2e9c52d04a131bfd6bfd57143f "Actinotelluria"               NA     
## f10abcfb58070db144ab557203b15112 "Blastococcus"                 NA     
## 2e3e409911947f6b58055dac76eafff2 "Gardnerella"                  NA     
## 6a8e34c34c852052fbb2ef47f31923cf "Bifidobacterium"              NA     
## 69b20ec4a1f82d5d7bfccce73e181144 "Aeriscardovia"                NA     
## 2f3464d9017dbcc3c07539e9e6d031d1 "Arthrobacter"                 NA     
## 19b23b503d10795479f12bed782e37bf "Helcobacillus"                NA     
## 13c1dc3da2ab678bb67e738463291f41 "Ornithinimicrobium"           NA     
## 0f7c178d133e189017d861892caf1b54 "Oryzihumus"                   NA     
## 0c416bb1ef62f13288e440253605f1f6 "Brevibacterium"               NA     
## a9ea27c012d71729be0af434b0135b8f "Kineococcus"                  NA     
## 9910430d69cf086a7a32730d88e36ca1 "Kineosporia"                  NA     
## bc5dc688aca3e85050859ccffb837227 "Trueperella"                  NA     
## 6cfcb015a00c6f3fb16e6eec63f4a35c "Micrococcus"                  NA     
## 1034ce7814ed4bb5c4506bc6b75eaa3f "Rothia"                       NA     
## 9dc76e20f768b3449b07c21ff7377623 "Leifsonia"                    NA     
## 4353875d14dabd7fe11946d21ac50b66 "Frondihabitans"               NA     
## 1c927fead59f669c939d603634ce60e3 "Labedella"                    NA     
## cc06b4a0146591e922e1f9c019a63485 "Pseudoclavibacter"            NA     
## c2b4b05dc7cde089c596aaaea2349b57 "Planktophila"                 NA     
## c0fcac392fda5b2c85f7eff24b4a08ed "Millisia"                     NA     
## fdc1a7c3ebe3c43c9205147181cadf6b "Corynebacterium"              NA     
## e229fd918de8f64d13ec2a69bab94a5d "Actinomadura"                 NA     
## af0d699336503dd28940bf80973df0d1 "Actinoallomurus"              NA     
## 7beb6afb10d4a33729f38eae58eb86fe "Ilumatobacter"                NA     
## 9f213cf8c7852cace5c0bae0997ca479 "Iamia"                        NA     
## e5516025a4d9f48a9fd7248989289b17 "Chroococcidiopsis"            NA     
## 265b94ca9e486aa0e39696dbf1004bab "Leptolyngbya"                 NA     
## fc5a4fb7042e9842c36f36e0ab934610 "Chroococcus"                  NA     
## c11850f778c3ed2aad77e905a962df9f "Pleurocapsa"                  NA     
## e1defeafac8215315915a82ed015dcb2 "Nostoc"                       NA     
## 4b4b20eeb4a4ccbd441b8d2ef9f31bf7 "Toxopsis"                     NA     
## 5575e3a3b9446bc439d3a13064c07e21 "Tolypothrix"                  NA     
## 565f359611711ce61076b0f3f8eb9453 "Cylindrospermum"              NA     
## 83196c5429def72c900061a0a8c5b49b "Brasilonema"                  NA     
## 0c6f8e3cb66947204cae236072a04a74 "Phormidium"                   NA     
## 2472bec6d09ab949b643cb1a4f41816b "Pseudanabaena"                NA     
## de5d66672c644945370a3bd62bd2caf4 "Phormidium"                   NA     
## 03ca951e561969caf45da606fde67866 "Coccomyxa"                    NA     
## d02aa15268aade892ad5dff83af3e7da "Chloroidium"                  NA     
## 3cd6ab4607d7c365dfdc11a48bf893c5 "Arthrospira"                  NA     
## 48b2489d2a8ef650129b144899cdf302 "Dunaliella"                   NA     
## 0040892ff482919cb88018e43a333cca "Acutodesmus"                  NA     
## a0051aa570b907944f08a912f8bc09fd "Avrainvillea"                 NA     
## d49b641988fea3844b9de1e6ad26ee98 "Hyphomicrobium"               NA     
## 14e8f8943c5595bbea2cca1cc3c383d0 "Geothrix"                     NA     
## d9b514bc64139095efef65a654a1d0e2 "Holophaga"                    NA     
## f54c0eca0d64aade6c60bbad968da659 "4-29"                         NA     
## 39e9884255a81dfa04b47a2b11e3ef5b "Phycisphaera"                 NA     
## aa33408e38ea9b07aa856e8e6701b0da "Granulicella"                 NA     
## cf7bf8f703a8335c0d3018f4604f1cb6 "Opitutus"                     NA     
## 31f232781685558bf9d62e35e8f237f9 "Akkermansia"                  NA     
## b8b9f753c83c855cc38aff497e5e89ce "DA101"                        NA     
## 85e29914e803ab4d6fb6602bd6b9ff00 "Candidatus Xiphinematobacter" NA     
## d37b60c688fcca90997aadce4c64d5a9 "Pedosphaera"                  NA     
## 107aca9889569069069d195bd8a31697 "Ellin506"                     NA     
## bd3849fc9106f9cdacb9341795c8cb29 "OR-59"                        NA     
## b5d0c6f1b9e8a8302389f77b79dcda85 "Chthoniobacter"               NA     
## bd1b5b2bb3a3f6cd721255c7a706da1c "Prosthecobacter"              NA     
## b9bad8448867f57e6a14c1a242c48774 "Haloferula"                   NA     
## b22df4733817d748ec348e7f3e6b33eb "Verrucomicrobium"             NA     
## 8941145147965d89bfcc4e88c0b9535b "heteroC45_4W"                 NA     
## 0d9178b0087a618145122137d5f02c9d "Thermacetogenium"             NA     
## 1d44015ea379303fcf6b84e6de3b56fe "Nostocoida"                   NA     
## abbfa75d6cee07b5d473575e6fc31ca6 "Candidatus Rhabdochlamydia"   NA     
## ebf9bf8eb6025551e0c72b979eadee03 "Simkania"                     NA     
## 46d7cb3e670b0a7c6be9f9e87b8a9062 "Parachlamydia"                NA     
## 77ade2a27cd5cf184bc7c566b5e40350 "Pyramidobacter"               NA     
## a0cdbcafbb2e9ca1d27ec77bf2e8d58d "Cloacibacillus"               NA     
## a79f2d2819aa6abbb25c3d52f0a6d88e "Mucispirillum"                NA     
## 9640db4284f6de2f96bc6a089999e1d9 "Turneriella"                  NA

Kphyseq.tax.level@sam_data

##           litter litter_number       sample sample_type    timing litter_type
## 10      ND Ind 2             5       KM?NN4       Pw-PD     fresh   Diarrhoea
## 11      ND Ind 3             6     WR6YN5 B        Pw-D     fresh   Diarrhoea
## 12      ND Ind 3             6      WR6NN11         W-R     fresh   Diarrhoea
## 13      ND Ind 3             6     WR6NN5 A       Pw-PD     fresh   Diarrhoea
## 14  Normal Ind 1            14       MC2NY7        Pw-N     fresh      Normal
## 23  Normal Ind 1            14      MC2NN10         W-N     fresh      Normal
## 24  Normal Ind 2            12    20-KH1NN4        Pw-N     fresh      Normal
## 25  Normal Ind 2            12   20-KH1NN10         W-N     fresh      Normal
## 26   ND Litter 1             7     LL?YN8 B        Pw-D overnight   Diarrhoea
## 27   ND Litter 2             8    CR?YN4 2A        Pw-D overnight   Diarrhoea
## 28   ND Litter 3             9     HC?YN4 B        Pw-D overnight   Diarrhoea
## 29   ND Litter 4            16      JE4YN11        Pw-D     fresh   Diarrhoea
## 30   ND Litter 6             1       NE?YN1        Pw-D overnight   Diarrhoea
## 31   ND Litter 7             2       SE3YN2        Pw-D     fresh   Diarrhoea
## 32   ND Litter 8            10       TE1YN7        Pw-D     fresh   Diarrhoea
## 33   ND Litter 9             3       JE3YN2        Pw-D     fresh   Diarrhoea
## 34  ND Litter 10             4    NH21-2YN2        Pw-D     fresh   Diarrhoea
## 35  ND Litter 11            13  NE22-?YN1 A        Pw-D     fresh   Diarrhoea
## 36  Normal Ind 3            11       AM4NN8        Pw-N     fresh      Normal
## 37  Normal Ind 3            11      AM4NN12         W-N     fresh      Normal
## 38  Normal Ind 4            12    20-KH2NN5        Pw-N     fresh      Normal
## 39   ND Litter 2             8      CR3NN10         W-R     fresh   Diarrhoea
## 40   ND Litter 3             9       HC1NN8         W-R     fresh   Diarrhoea
## 41   ND Litter 4            16    JE?NN12 B         W-R overnight   Diarrhoea
## 42   ND Litter 6             1       NE4NN6         W-R     fresh   Diarrhoea
## 43   ND Litter 7             2      SE3NN11         W-R     fresh   Diarrhoea
## 44   ND Litter 8            10    TE?NN11 A         W-R overnight   Diarrhoea
## 45   ND Litter 9             3       JE2NN8         W-R     fresh   Diarrhoea
## 46  ND Litter 10             4   NH21-3NN12         W-R     fresh   Diarrhoea
## 47  ND Litter 11            13   NE22-5NN10         W-R     fresh   Diarrhoea
## 48  Normal Ind 4            12   20-KH2NN12         W-N     fresh      Normal
## 49  Normal Ind 5            12    20-KH3NN5        Pw-N     fresh      Normal
## 5       ND Ind 1            15     NH4YN7 B        Pw-D     fresh   Diarrhoea
## 50  Normal Ind 5            12 20-KH3NN10 B         W-N     fresh      Normal
## 6       ND Ind 1            15       NH4NY9         W-R     fresh   Diarrhoea
## 62   ND Litter 2             8    CR?NN4 v1       Pw-PD overnight   Diarrhoea
## 63   ND Litter 3             9       HC?NN2       Pw-PD overnight   Diarrhoea
## 65   ND Litter 6             1       NE?NN1       Pw-PD overnight   Diarrhoea
## 66   ND Litter 7             2     SE?NN1 C       Pw-PD overnight   Diarrhoea
## 67   ND Litter 8            10     TE?NN5 A       Pw-PD overnight   Diarrhoea
## 68   ND Litter 9             3     JE?NN1 A       Pw-PD     fresh   Diarrhoea
## 69  ND Litter 10             4    NH21-?NN1       Pw-PD overnight   Diarrhoea
## 7       ND Ind 1            15      NH?NN6A       Pw-PD overnight   Diarrhoea
## 70  ND Litter 11            13  NE22-?NN1 A       Pw-PD     fresh   Diarrhoea
## 71   ND Litter 1             7      LL4NN11         W-R     fresh   Diarrhoea
## 8       ND Ind 2             5       KM2YY6        Pw-D     fresh   Diarrhoea
## 9       ND Ind 2             5      KM2NN10         W-R     fresh   Diarrhoea
## a61  ND Litter 1             7       LL?NN6       Pw-PD     fresh   Diarrhoea
## a64  ND Litter 4            16      JE?NN6A       Pw-PD overnight   Diarrhoea
##     kittenID sample_cat diarrhoea treatment    owner   breed        dob
## 10    litter     litter         N         N Breeder2 Burmese 21/01/2019
## 11         6 individual         Y         N Breeder1 Siamese 22/08/2018
## 12         6 individual         N         N Breeder1 Siamese 22/08/2018
## 13         6 individual         N         N Breeder1 Siamese 22/08/2018
## 14         2 individual         N         Y Breeder2 Burmese  9/03/2019
## 23         2 individual         N         N Breeder2 Burmese  9/03/2019
## 24         1 individual         N         N      FNU     DSH 18/04/2020
## 25         1 individual         N         N      FNU     DSH 18/04/2020
## 26    litter     litter         Y         N Breeder3 Burmese  7/02/2019
## 27    litter     litter         Y         N Breeder1 Siamese 27/08/2018
## 28    litter     litter         Y         N Breeder1 Siamese  6/08/2018
## 29         4     litter         Y         N      FNU     DSH  7/03/2019
## 30    litter     litter         Y         N      FNU     DSH  8/11/2020
## 31         3     litter         Y         N      FNU     DSH  4/11/2020
## 32         1     litter         Y         N      FNU     DSH 13/03/2019
## 33         3     litter         Y         N      FNU     DSH 11/03/2021
## 34         2     litter         Y         N      FNU     DSH 13/08/2021
## 35    litter     litter         Y         N      FNU     DSH 17/02/2022
## 36         4 individual         N         N Breeder3 Burmese 11/02/2019
## 37         4 individual         N         N Breeder3 Burmese 11/02/2019
## 38         2 individual         N         N      FNU     DSH 18/04/2020
## 39         3     litter         N         N Breeder1 Siamese 27/08/2018
## 40         1     litter         N         N Breeder1 Siamese  6/08/2018
## 41    litter     litter         N         N      FNU     DSH  7/03/2019
## 42         4     litter         N         N      FNU     DSH  8/11/2020
## 43         3     litter         N         N      FNU     DSH  4/11/2020
## 44    litter     litter         N         N      FNU     DSH 13/03/2019
## 45         2     litter         N         N      FNU     DSH 11/03/2021
## 46         3     litter         N         N      FNU     DSH 13/08/2021
## 47         5     litter         N         N      FNU     DSH 17/02/2022
## 48         2 individual         N         N      FNU     DSH 18/04/2020
## 49         3 individual         N         N      FNU     DSH 18/04/2020
## 5          4     litter         Y         Y      FNU     DSH 11/03/2019
## 50         3 individual         N         N      FNU     DSH 18/04/2020
## 6          4     litter         N         Y      FNU     DSH 11/03/2019
## 62    litter     litter         N         N Breeder1 Siamese 27/08/2018
## 63    litter     litter         N         N Breeder1 Siamese  6/08/2018
## 65    litter     litter         N         N      FNU     DSH  8/11/2020
## 66    litter     litter         N         N      FNU     DSH  4/11/2020
## 67    litter     litter         N         N      FNU     DSH 13/03/2019
## 68    litter     litter         N         N      FNU     DSH 11/03/2021
## 69    litter     litter         N         N      FNU     DSH 13/08/2021
## 7     litter     litter         N         N      FNU     DSH 11/03/2019
## 70    litter     litter         N         N      FNU     DSH 17/02/2022
## 71         4     litter         N         N Breeder3 Burmese  7/02/2019
## 8          2     litter         Y         Y Breeder2 Burmese 21/01/2019
## 9          2     litter         N         N Breeder2 Burmese 21/01/2019
## a61   litter     litter         N         N Breeder3 Burmese  7/02/2019
## a64   litter     litter         N         N      FNU     DSH  7/03/2019
##     weaning_date age_weaned_wk age_weaned_day date_collected week age_wk
## 10     8/04/2019            11             77      4/03/2019    4      6
## 11    12/11/2018            12             82      9/10/2018    5      7
## 12    12/11/2018            12             82     20/11/2018   11     13
## 13    12/11/2018            12             82      9/10/2018    5      7
## 14    11/05/2019             9             63     24/04/2019    7      7
## 23    11/05/2019             9             63     15/05/2019   10     10
## 24    11/06/2020             8             54     12/06/2020    4      8
## 25    11/06/2020             8             54     23/07/2020   10     14
## 26     1/05/2019            12             83      3/04/2019    8      8
## 27     7/11/2018            10             72      6/10/2018    4      6
## 28    28/09/2018             8             53      3/10/2018    4      8
## 29    17/04/2019             6             41     21/05/2019   11     11
## 30     4/01/2021             8             57      9/12/2020    1      4
## 31     4/01/2021             9             61      8/12/2020    2      5
## 32    17/04/2019             5             35     26/04/2019    7      6
## 33     1/06/2021            12             82     20/04/2021    2      6
## 34    10/10/2021             8             58     30/09/2021    2      7
## 35     6/05/2022            11             78     24/03/2022    1      5
## 36     1/05/2019            11             79      3/04/2019    8      7
## 37     1/05/2019            11             79      1/05/2019   12     11
## 38    11/06/2020             8             54     18/06/2020    5      9
## 39     7/11/2018            10             72     13/11/2018   10     11
## 40    28/09/2018             8             53     30/10/2018    8     12
## 41    17/04/2019             6             41     28/05/2019   12     12
## 42     4/01/2021             8             57     12/01/2021    6      9
## 43     4/01/2021             9             61     11/02/2021   11     14
## 44    17/04/2019             5             35     21/05/2019   11     10
## 45     1/06/2021            12             82      2/06/2021    8     12
## 46    10/10/2021             8             58      9/12/2021   12     17
## 47     6/05/2022            11             78     26/05/2022   10     14
## 48    11/06/2020             8             54      3/08/2020   12     15
## 49    11/06/2020             8             54     18/06/2020    5      9
## 5     17/04/2019             5             37     26/04/2019    7      7
## 50    11/06/2020             8             54     24/07/2020   10     14
## 6     17/04/2019             5             37      7/05/2019    9      8
## 62     7/11/2018            10             72      4/10/2018    4      5
## 63    28/09/2018             8             53     19/09/2018    2      6
## 65     4/01/2021             8             57      9/12/2020    1      4
## 66     4/01/2021             9             61      3/12/2020    1      4
## 67    17/04/2019             5             35     10/04/2019    5      4
## 68     1/06/2021            12             82     13/04/2021    1      5
## 69    10/10/2021             8             58     17/09/2021    1      5
## 7     17/04/2019             5             37     17/04/2019    6      5
## 70     6/05/2022            11             78     24/03/2022    1      5
## 71     1/05/2019            12             83     24/04/2019   11     11
## 8      8/04/2019            11             77     18/03/2019    6      8
## 9      8/04/2019            11             77     15/04/2019    6     12
## a61    1/05/2019            12             83     20/03/2019    6      6
## a64   17/04/2019             6             41     17/04/2019    6      6
##     age_day sample.....weaning Date_solids_started wk_solids_started
## 10       42                 -5          25/02/2019                 5
## 11       48                 -5           3/10/2018                 6
## 12       90                  1           3/10/2018                 6
## 13       48                 -5           3/10/2018                 6
## 14       46                 -2          17/04/2019                 6
## 23       67                  1          17/04/2019                 6
## 24       55                  0          22/05/2020                 5
## 25       96                  6          22/05/2020                 5
## 26       55                 -4          11/03/2019                 5
## 27       40                 -5           4/10/2018                 5
## 28       58                  1          19/09/2018                 6
## 29       75                  5           2/04/2019                 4
## 30       31                 -4           7/12/2020                 4
## 31       34                 -4           1/12/2020                 4
## 32       44                  1           2/04/2019                 3
## 33       40                 -6          13/04/2021                 5
## 34       48                 -1          24/09/2021                 6
## 35       35                 -6          14/03/2022                 4
## 36       51                 -4          29/03/2019                 7
## 37       79                  0          29/03/2019                 7
## 38       61                  1          22/05/2020                 5
## 39       78                  1           4/10/2018                 5
## 40       85                  5          19/09/2018                 6
## 41       82                  6           2/04/2019                 4
## 42       65                  1           7/12/2020                 4
## 43       99                  5           1/12/2020                 4
## 44       69                  5           2/04/2019                 3
## 45       83                  0          13/04/2021                 5
## 46      118                  9          24/09/2021                 6
## 47       98                  3          14/03/2022                 4
## 48      107                  8          22/05/2020                 5
## 49       61                  1          22/05/2020                 5
## 5        46                  1           2/04/2019                 3
## 50       97                  6          22/05/2020                 5
## 6        57                  3           2/04/2019                 3
## 62       38                 -5           4/10/2018                 5
## 63       44                 -1          19/09/2018                 6
## 65       31                 -4           7/12/2020                 4
## 66       29                 -5           1/12/2020                 4
## 67       28                 -1           2/04/2019                 3
## 68       33                 -7          13/04/2021                 5
## 69       35                 -3          24/09/2021                 6
## 7        37                  0           2/04/2019                 3
## 70       35                 -6          14/03/2022                 4
## 71       76                 -1          11/03/2019                 5
## 8        56                 -3          25/02/2019                 5
## 9        84                  1          25/02/2019                 5
## a61      41                 -6          11/03/2019                 5
## a64      41                  0           2/04/2019                 4
##     day_solids_started nursing...                  site            medication
## 10                  35          1 Genevieve kitten room                  <NA>
## 11                  42          1                 Levin                  <NA>
## 12                  42          7                 Levin                  <NA>
## 13                  42          1                 Levin                  <NA>
## 14                  39          1 Genevieve kitten room      queen on panacur
## 23                  39          4 Genevieve kitten room Chlorsig night before
## 24                  34          3       FNU kitten room                  <NA>
## 25                  34          9       FNU kitten room                  <NA>
## 26                  32          3      CY house bedroom                  <NA>
## 27                  38          0                    PN                  <NA>
## 28                  44          2                 Levin                  <NA>
## 29                  26          7       Qaurintine room                  <NA>
## 30                  29          0                   FNU                  <NA>
## 31                  27          1                   FNU                  <NA>
## 32                  20          3       Qaurintine room                  <NA>
## 33                  33          1                   FNU                  <NA>
## 34                  42          1   Hallway kitten room                  <NA>
## 35                  25          1   Hallway kitten room                  <NA>
## 36                  46          1      CY house bedroom                  <NA>
## 37                  46          5      CY house bedroom                  <NA>
## 38                  34          4       FNU kitten room                  <NA>
## 39                  38          6               Cahills                  <NA>
## 40                  44          6                 Levin                  <NA>
## 41                  26          8       Qaurintine room                  <NA>
## 42                  29          5              day room                  <NA>
## 43                  27         10                   FNU                  <NA>
## 44                  20          7       Qaurintine room                  <NA>
## 45                  33          7                   FNU                  <NA>
## 46                  42         11   Hallway kitten room                  <NA>
## 47                  25         10   Hallway kitten room                  <NA>
## 48                  34         10         Saw dust room                  <NA>
## 49                  34          4       FNU kitten room                  <NA>
## 5                   22          3       Qaurintine room           Antibiotics
## 50                  34          9       FNU kitten room                  <NA>
## 6                   22          5       Qaurintine room           Antibiotics
## 62                  38          0                    PN                  <NA>
## 63                  44          0                 Levin                  <NA>
## 65                  29          0                   FNU                  <NA>
## 66                  27          0                   FNU                  <NA>
## 67                  20          1       Qaurintine room                  <NA>
## 68                  33          0   Hallway kitten room                  <NA>
## 69                  42         -1   Hallway kitten room                  <NA>
## 7                   22          2       Qaurintine room                  <NA>
## 70                  25          1   Hallway kitten room                  <NA>
## 71                  32          6      CY house bedroom                  <NA>
## 8                   35          3 Genevieve kitten room               Panacur
## 9                   35          7   Catery out the back                  <NA>
## a61                 32          1      CY house bedroom                  <NA>
## a64                 26          2       Qaurintine room                  <NA>
##                    mdiet                kdiet weaning_status
## 10        wet + biscuits       wet + biscuits   peri-weaning
## 11  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 12  raw + wet + biscuits raw + wet + biscuits         weaned
## 13  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 14        wet + biscuits       wet + biscuits   peri-weaning
## 23        wet + biscuits       wet + biscuits         weaned
## 24        wet + biscuits       wet + biscuits         weaned
## 25        wet + biscuits       wet + biscuits         weaned
## 26  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 27  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 28  raw + wet + biscuits raw + wet + biscuits         weaned
## 29        wet + biscuits       wet + biscuits         weaned
## 30        wet + biscuits       wet + biscuits   peri-weaning
## 31        wet + biscuits       wet + biscuits   peri-weaning
## 32        wet + biscuits       wet + biscuits         weaned
## 33        wet + biscuits       wet + biscuits   peri-weaning
## 34        wet + biscuits       wet + biscuits   peri-weaning
## 35        wet + biscuits       wet + biscuits   peri-weaning
## 36  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 37  raw + wet + biscuits raw + wet + biscuits         weaned
## 38        wet + biscuits       wet + biscuits         weaned
## 39  raw + wet + biscuits raw + wet + biscuits         weaned
## 40  raw + wet + biscuits raw + wet + biscuits         weaned
## 41        wet + biscuits       wet + biscuits         weaned
## 42        wet + biscuits       wet + biscuits         weaned
## 43        wet + biscuits       wet + biscuits         weaned
## 44        wet + biscuits       wet + biscuits         weaned
## 45        wet + biscuits       wet + biscuits         weaned
## 46        wet + biscuits       wet + biscuits         weaned
## 47        wet + biscuits       wet + biscuits         weaned
## 48        wet + biscuits       wet + biscuits         weaned
## 49        wet + biscuits       wet + biscuits         weaned
## 5         wet + biscuits       wet + biscuits         weaned
## 50        wet + biscuits       wet + biscuits         weaned
## 6         wet + biscuits       wet + biscuits         weaned
## 62  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 63  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 65        wet + biscuits       wet + biscuits   peri-weaning
## 66        wet + biscuits       wet + biscuits   peri-weaning
## 67        wet + biscuits       wet + biscuits   peri-weaning
## 68        wet + biscuits       wet + biscuits   peri-weaning
## 69        wet + biscuits       wet + biscuits        nursing
## 7         wet + biscuits       wet + biscuits   peri-weaning
## 70        wet + biscuits       wet + biscuits   peri-weaning
## 71  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 8         wet + biscuits       wet + biscuits   peri-weaning
## 9         wet + biscuits       wet + biscuits         weaned
## a61 raw + wet + biscuits raw + wet + biscuits   peri-weaning
## a64       wet + biscuits       wet + biscuits   peri-weaning

Kphyseq.tax.level@sam_data[Kphyseq.tax.level@sam_data$sample_type == "Pw-PD",]

##           litter litter_number      sample sample_type    timing litter_type
## 10      ND Ind 2             5      KM?NN4       Pw-PD     fresh   Diarrhoea
## 13      ND Ind 3             6    WR6NN5 A       Pw-PD     fresh   Diarrhoea
## 62   ND Litter 2             8   CR?NN4 v1       Pw-PD overnight   Diarrhoea
## 63   ND Litter 3             9      HC?NN2       Pw-PD overnight   Diarrhoea
## 65   ND Litter 6             1      NE?NN1       Pw-PD overnight   Diarrhoea
## 66   ND Litter 7             2    SE?NN1 C       Pw-PD overnight   Diarrhoea
## 67   ND Litter 8            10    TE?NN5 A       Pw-PD overnight   Diarrhoea
## 68   ND Litter 9             3    JE?NN1 A       Pw-PD     fresh   Diarrhoea
## 69  ND Litter 10             4   NH21-?NN1       Pw-PD overnight   Diarrhoea
## 7       ND Ind 1            15     NH?NN6A       Pw-PD overnight   Diarrhoea
## 70  ND Litter 11            13 NE22-?NN1 A       Pw-PD     fresh   Diarrhoea
## a61  ND Litter 1             7      LL?NN6       Pw-PD     fresh   Diarrhoea
## a64  ND Litter 4            16     JE?NN6A       Pw-PD overnight   Diarrhoea
##     kittenID sample_cat diarrhoea treatment    owner   breed        dob
## 10    litter     litter         N         N Breeder2 Burmese 21/01/2019
## 13         6 individual         N         N Breeder1 Siamese 22/08/2018
## 62    litter     litter         N         N Breeder1 Siamese 27/08/2018
## 63    litter     litter         N         N Breeder1 Siamese  6/08/2018
## 65    litter     litter         N         N      FNU     DSH  8/11/2020
## 66    litter     litter         N         N      FNU     DSH  4/11/2020
## 67    litter     litter         N         N      FNU     DSH 13/03/2019
## 68    litter     litter         N         N      FNU     DSH 11/03/2021
## 69    litter     litter         N         N      FNU     DSH 13/08/2021
## 7     litter     litter         N         N      FNU     DSH 11/03/2019
## 70    litter     litter         N         N      FNU     DSH 17/02/2022
## a61   litter     litter         N         N Breeder3 Burmese  7/02/2019
## a64   litter     litter         N         N      FNU     DSH  7/03/2019
##     weaning_date age_weaned_wk age_weaned_day date_collected week age_wk
## 10     8/04/2019            11             77      4/03/2019    4      6
## 13    12/11/2018            12             82      9/10/2018    5      7
## 62     7/11/2018            10             72      4/10/2018    4      5
## 63    28/09/2018             8             53     19/09/2018    2      6
## 65     4/01/2021             8             57      9/12/2020    1      4
## 66     4/01/2021             9             61      3/12/2020    1      4
## 67    17/04/2019             5             35     10/04/2019    5      4
## 68     1/06/2021            12             82     13/04/2021    1      5
## 69    10/10/2021             8             58     17/09/2021    1      5
## 7     17/04/2019             5             37     17/04/2019    6      5
## 70     6/05/2022            11             78     24/03/2022    1      5
## a61    1/05/2019            12             83     20/03/2019    6      6
## a64   17/04/2019             6             41     17/04/2019    6      6
##     age_day sample.....weaning Date_solids_started wk_solids_started
## 10       42                 -5          25/02/2019                 5
## 13       48                 -5           3/10/2018                 6
## 62       38                 -5           4/10/2018                 5
## 63       44                 -1          19/09/2018                 6
## 65       31                 -4           7/12/2020                 4
## 66       29                 -5           1/12/2020                 4
## 67       28                 -1           2/04/2019                 3
## 68       33                 -7          13/04/2021                 5
## 69       35                 -3          24/09/2021                 6
## 7        37                  0           2/04/2019                 3
## 70       35                 -6          14/03/2022                 4
## a61      41                 -6          11/03/2019                 5
## a64      41                  0           2/04/2019                 4
##     day_solids_started nursing...                  site medication
## 10                  35          1 Genevieve kitten room       <NA>
## 13                  42          1                 Levin       <NA>
## 62                  38          0                    PN       <NA>
## 63                  44          0                 Levin       <NA>
## 65                  29          0                   FNU       <NA>
## 66                  27          0                   FNU       <NA>
## 67                  20          1       Qaurintine room       <NA>
## 68                  33          0   Hallway kitten room       <NA>
## 69                  42         -1   Hallway kitten room       <NA>
## 7                   22          2       Qaurintine room       <NA>
## 70                  25          1   Hallway kitten room       <NA>
## a61                 32          1      CY house bedroom       <NA>
## a64                 26          2       Qaurintine room       <NA>
##                    mdiet                kdiet weaning_status
## 10        wet + biscuits       wet + biscuits   peri-weaning
## 13  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 62  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 63  raw + wet + biscuits raw + wet + biscuits   peri-weaning
## 65        wet + biscuits       wet + biscuits   peri-weaning
## 66        wet + biscuits       wet + biscuits   peri-weaning
## 67        wet + biscuits       wet + biscuits   peri-weaning
## 68        wet + biscuits       wet + biscuits   peri-weaning
## 69        wet + biscuits       wet + biscuits        nursing
## 7         wet + biscuits       wet + biscuits   peri-weaning
## 70        wet + biscuits       wet + biscuits   peri-weaning
## a61 raw + wet + biscuits raw + wet + biscuits   peri-weaning
## a64       wet + biscuits       wet + biscuits   peri-weaning

colSums(Kphyseq.tax.level@otu_table)

##    10    11    12    13    14    23    24    25    26    27    28    29    30 
## 77742 50715 71124 75685 52757 35533 15887 36901 45104 39235 31112 61767 34095 
##    31    32    33    34    35    36    37    38    39    40    41    42    43 
## 47768 69142 33168 55177 51753 41583 43099 25375 48774 57293 64862 31003 56873 
##    44    45    46    47    48    49     5    50     6    62    63    65    66 
## 48234 55614 50909 55065 56661 61779 81689 70145 56336 63554 70758 47569 36623 
##    67    68    69     7    70    71     8     9   a61   a64 
## 43765 39515 46707 49432 67719 69897 38256 67082 60880 30219

sample_variables(Kphyseq.tax.level)

##  [1] "litter"              "litter_number"       "sample"             
##  [4] "sample_type"         "timing"              "litter_type"        
##  [7] "kittenID"            "sample_cat"          "diarrhoea"          
## [10] "treatment"           "owner"               "breed"              
## [13] "dob"                 "weaning_date"        "age_weaned_wk"      
## [16] "age_weaned_day"      "date_collected"      "week"               
## [19] "age_wk"              "age_day"             "sample.....weaning" 
## [22] "Date_solids_started" "wk_solids_started"   "day_solids_started" 
## [25] "nursing..."          "site"                "medication"         
## [28] "mdiet"               "kdiet"               "weaning_status"

# filter out low abundance data
Kphyseq.tax.level <- phyloseq_filter_prevalence(Kphyseq.tax.level, prev.trh = 0.05, abund.trh = 100, threshold_condition = "AND", abund.type = "total")  

#prev.trh   = Prevalence threshold (default, 0.05 = 5% of samples)
#abund.trh = Abundance threshold (default, NULL). Abundance threshold defines if the OTU should be preserved if its abundance is larger than threshold (e.g., >= 50 reads)
#threshold_condition    = Indicates whether OTU should be kept if it occurs in many samples AND/OR it has high abundance - type of prevalence and abundance conditions, can be "OR" (default) or "AND"
#abund.type= Character string indicating which type of OTU abundance to take into account for filtering ("total", "mean", or "median")

otu_data <- as.matrix(Kphyseq.tax.level@otu_table@.Data)
otu_data <- t(otu_data)
otu_data <- as.data.frame(otu_data)

meta_data <- as.matrix(Kphyseq.tax.level@sam_data)
meta_data <- as.data.frame(meta_data)

###############################################################
## Setting up colour palette
qual_col_pals <- brewer.pal.info[brewer.pal.info$category == 'qual',]   ##  Set up colour libary
col_vector <- unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
group_colours <- sample(col_vector, length(levels(as.factor(meta_data$Treatment))))
cols <- group_colours[as.factor(meta_data$Treatment)]

## PCoA
dist = phyloseq::distance(Kphyseq.tax.level, method="bray")
ordination = ordinate(Kphyseq, method="PCoA", distance=dist)
plot_ordination(Kphyseq, ordination, color="sample_type") + 
  theme_classic() +
  theme(strip.background = element_blank())

## PCoA suing base R - cmdscale = Classical multidimensional scaling (MDS) of a data matrix. Also known as principal coordinates analysis (Gower, 1966). PCoA focuses on distances, and it tries to extract the dimensions that account for the maximum distances.
pcoa.res <- cmdscale(vegdist(otu_data, method = "bray"), k = 3, eig = T, add = T)

## PLotting PCoA 
#plot(pcoa.res$points[,1],pcoa.res$points[,2],cex=2, bg = cols, pch = 21, frame=F,lwd=1,cex.axis=1.4,cex.lab=1.4,
#     xlab=paste("\nPC1 (",round(pcoa.res$eig*100/sum(pcoa.res$eig),1)[1],"%)",sep=""),
#     ylab=paste("\nPC2 (",round(pcoa.res$eig*100/sum(pcoa.res$eig),1)[2],"%)",sep="")) +
#  box(bty="l",lwd=3)

#devtools::install_github("kassambara/factoextra")
library(factoextra)

## Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa

## PCA - testing out 2 plotting methods, factoextra or using base R. 
#PCA focuses on shared variance: it tries to summarize multiple variables in the minimum number of components so that each component explains the most variance

# caluclating the PCA
pca <- prcomp(otu_data, scale=T)

# Looking at variables and scree plots 
var <- get_pca_var(pca)
var

## Principal Component Analysis Results for variables
##  ===================================================
##   Name       Description                                    
## 1 "$coord"   "Coordinates for the variables"                
## 2 "$cor"     "Correlations between variables and dimensions"
## 3 "$cos2"    "Cos2 for the variables"                       
## 4 "$contrib" "contributions of the variables"

head(var$contrib)

##                                       Dim.1      Dim.2        Dim.3      Dim.4
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.99133881 0.45614369 3.642328e-01 0.78514069
## ec4dafd949562cb1c67abf1edb908e45 1.29717694 0.01550891 1.170733e-01 0.22579697
## b1cc0afab8aabe335f3d2183a8f862a8 1.71839186 0.03824469 4.468427e-05 0.18780578
## b3f7ce9240052a0925ec9e675b5c5801 1.93992591 0.11594028 3.319966e-03 0.01584156
## 1ef109986a98fbad2514a0bdde298328 0.03763307 3.42961024 3.085988e+00 2.59209992
## 9cbea8ff52e16e14d63f27d5f6f9ee70 1.10979434 0.40604714 2.812402e-04 2.49633712
##                                         Dim.5        Dim.6        Dim.7
## 81ca8fa4a795e9929b18c343fa7e5d6d 1.4819724349 1.1160745617 0.1152091978
## ec4dafd949562cb1c67abf1edb908e45 1.0313042892 0.2465431634 0.0315765608
## b1cc0afab8aabe335f3d2183a8f862a8 0.3877467479 0.1754777260 0.0005895772
## b3f7ce9240052a0925ec9e675b5c5801 0.0272060070 0.0096039999 0.0116769217
## 1ef109986a98fbad2514a0bdde298328 0.0002095305 0.0002278446 0.8941002019
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.8489500014 2.4800138050 0.2231236436
##                                         Dim.8      Dim.9       Dim.10
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.0324233016 0.01744615 2.361473e-01
## ec4dafd949562cb1c67abf1edb908e45 0.4020349552 0.09600739 4.465574e-02
## b1cc0afab8aabe335f3d2183a8f862a8 0.0486447856 0.00145492 1.996208e-01
## b3f7ce9240052a0925ec9e675b5c5801 0.0007407732 0.02585790 4.395408e-07
## 1ef109986a98fbad2514a0bdde298328 2.6954574122 1.72003915 1.924115e-04
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.0445532679 0.02896760 3.609794e-01
##                                       Dim.11     Dim.12       Dim.13
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.071818827 0.26682880 0.9483523047
## ec4dafd949562cb1c67abf1edb908e45 0.008556601 1.21053689 2.6943417036
## b1cc0afab8aabe335f3d2183a8f862a8 0.977271886 0.03062932 0.6098532008
## b3f7ce9240052a0925ec9e675b5c5801 0.064520433 0.02191747 0.0005528226
## 1ef109986a98fbad2514a0bdde298328 0.015908370 0.08434262 0.5944299005
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.197988248 1.11191196 0.2933101662
##                                        Dim.14     Dim.15       Dim.16
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.2631087836 0.10126818 0.6916258595
## ec4dafd949562cb1c67abf1edb908e45 0.6818424624 0.80026285 0.3441446454
## b1cc0afab8aabe335f3d2183a8f862a8 0.0107894363 0.02120740 0.1327334217
## b3f7ce9240052a0925ec9e675b5c5801 0.0012749420 0.04225956 0.0759392759
## 1ef109986a98fbad2514a0bdde298328 1.0126549663 0.88502334 0.8232562705
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.0004766762 0.02836171 0.0006720674
##                                       Dim.17      Dim.18      Dim.19
## 81ca8fa4a795e9929b18c343fa7e5d6d 2.105124829 1.366161654 1.681728369
## ec4dafd949562cb1c67abf1edb908e45 0.943217358 0.166833713 1.246926299
## b1cc0afab8aabe335f3d2183a8f862a8 0.112399287 0.327966851 0.051972983
## b3f7ce9240052a0925ec9e675b5c5801 0.132448382 0.009161588 0.004901838
## 1ef109986a98fbad2514a0bdde298328 0.007922522 0.059450168 0.020889020
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.920686586 0.000191096 0.184934028
##                                       Dim.20     Dim.21      Dim.22      Dim.23
## 81ca8fa4a795e9929b18c343fa7e5d6d 1.484045310 0.04092130 0.693081912 0.235694943
## ec4dafd949562cb1c67abf1edb908e45 0.003380843 0.02335840 0.106797340 0.201070445
## b1cc0afab8aabe335f3d2183a8f862a8 0.219963258 0.03100119 0.267110233 0.061784911
## b3f7ce9240052a0925ec9e675b5c5801 0.008215939 0.02478590 0.014116942 0.006435548
## 1ef109986a98fbad2514a0bdde298328 0.309935157 0.23132896 0.006678032 0.092184949
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.381331546 0.05710211 1.059878764 0.031031080
##                                       Dim.24     Dim.25     Dim.26       Dim.27
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.662302893 0.02934144 0.54525802 3.345670e-03
## ec4dafd949562cb1c67abf1edb908e45 0.371550745 0.06090551 0.08621185 6.099378e-04
## b1cc0afab8aabe335f3d2183a8f862a8 0.515185636 0.01670611 0.12311612 5.494894e-01
## b3f7ce9240052a0925ec9e675b5c5801 0.007047173 0.01928606 0.03528348 5.562205e-05
## 1ef109986a98fbad2514a0bdde298328 0.011372173 0.09159426 0.02756274 1.339824e-02
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.058335995 0.11465810 0.02567864 3.457176e-02
##                                      Dim.28      Dim.29      Dim.30     Dim.31
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.22056618 0.159496877 0.026285420 0.74832961
## ec4dafd949562cb1c67abf1edb908e45 1.05370467 0.073534430 0.577498743 0.37598003
## b1cc0afab8aabe335f3d2183a8f862a8 0.59373830 0.369446428 0.001759332 0.05954969
## b3f7ce9240052a0925ec9e675b5c5801 0.02608621 0.083650268 0.003413911 0.40290511
## 1ef109986a98fbad2514a0bdde298328 0.02526283 0.874224269 0.195834707 0.09477652
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.06234552 0.006053637 0.031131171 3.08904266
##                                      Dim.32      Dim.33     Dim.34     Dim.35
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.03951025 1.020543116 0.10086962 3.01107568
## ec4dafd949562cb1c67abf1edb908e45 0.66653903 0.588766936 2.29493097 0.56171016
## b1cc0afab8aabe335f3d2183a8f862a8 0.02480338 0.126411151 0.09464603 0.01082605
## b3f7ce9240052a0925ec9e675b5c5801 0.08125452 0.010382105 0.23782079 0.50790257
## 1ef109986a98fbad2514a0bdde298328 1.79766288 0.828053532 0.64128973 3.15756803
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.05542938 0.001488246 0.05053153 0.17311244
##                                        Dim.36       Dim.37     Dim.38
## 81ca8fa4a795e9929b18c343fa7e5d6d 3.984619e-03 3.5435643846 0.28092574
## ec4dafd949562cb1c67abf1edb908e45 3.014952e-01 0.0428825797 0.18163044
## b1cc0afab8aabe335f3d2183a8f862a8 1.140902e-02 0.0805191290 0.15689718
## b3f7ce9240052a0925ec9e675b5c5801 3.296466e-02 0.0002418222 0.02332261
## 1ef109986a98fbad2514a0bdde298328 5.897139e-02 1.9126121012 0.16954077
## 9cbea8ff52e16e14d63f27d5f6f9ee70 8.165878e-05 0.0806269522 0.54728741
##                                      Dim.39     Dim.40    Dim.41     Dim.42
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.84066915 0.13466278 0.4891507 1.46769527
## ec4dafd949562cb1c67abf1edb908e45 0.10944051 1.26820599 0.2077982 0.35818677
## b1cc0afab8aabe335f3d2183a8f862a8 0.10512062 0.13101858 0.7892217 0.53857883
## b3f7ce9240052a0925ec9e675b5c5801 0.26729308 0.09834058 0.1410963 0.23988890
## 1ef109986a98fbad2514a0bdde298328 0.08279706 1.87189404 1.9459330 0.06785926
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.38149245 0.20320898 0.1336117 0.35200644
##                                       Dim.43      Dim.44     Dim.45
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.007642705 1.810808985 1.27141450
## ec4dafd949562cb1c67abf1edb908e45 0.013962026 0.024767869 0.06516522
## b1cc0afab8aabe335f3d2183a8f862a8 0.599097705 0.292863003 0.06936333
## b3f7ce9240052a0925ec9e675b5c5801 0.436130349 0.420238340 0.15507621
## 1ef109986a98fbad2514a0bdde298328 2.144055297 4.377650139 9.41056412
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.077727765 0.006702592 2.36474947
##                                        Dim.46       Dim.47      Dim.48
## 81ca8fa4a795e9929b18c343fa7e5d6d 0.3186201452 0.0402092983 0.017587430
## ec4dafd949562cb1c67abf1edb908e45 0.2334219437 0.0004454219 0.002960035
## b1cc0afab8aabe335f3d2183a8f862a8 1.1845988100 0.2910916186 0.114618827
## b3f7ce9240052a0925ec9e675b5c5801 0.0006471038 0.1885303769 0.018252652
## 1ef109986a98fbad2514a0bdde298328 2.0022877598 0.3584233180 6.245092048
## 9cbea8ff52e16e14d63f27d5f6f9ee70 0.1586563323 0.7411641697 0.090524586
##                                      Dim.49
## 81ca8fa4a795e9929b18c343fa7e5d6d 11.2692785
## ec4dafd949562cb1c67abf1edb908e45  1.8389099
## b1cc0afab8aabe335f3d2183a8f862a8  2.1135890
## b3f7ce9240052a0925ec9e675b5c5801  0.5596421
## 1ef109986a98fbad2514a0bdde298328  0.1592758
## 9cbea8ff52e16e14d63f27d5f6f9ee70  3.4035705

fviz_pca_var(pca, col.var = "black")

fviz_pca_var(pca, col.var="contrib",
             gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
             repel = TRUE # Avoid text overlapping
)

fviz_contrib(pca, choice = "var", axes = 1, top = 10)   

#pdf("Kphyseq_PCA.pdf",height=6,width=8,pointsize=15)  
fviz_pca_ind(pca,
             habillage = meta_data$sample_type, # color by sample type
             addEllipses = T, 
             ellipse.level=0.95,
             legend.title = "Sample type",
             repel = F,
             pointsize = 3,
             label = "none",
             geom="point",
             invisible="quali",
             ggtheme = theme_bw())

#dev.off() 

###### Working to PLSDA ########################################################################
## using base R 
grp <- "sample_type"
cols <- c("cornflowerblue","gold", "orange", "purple", "green", "pink")[as.factor(meta_data[,grp])]

eigs <- pca$sdev^2
eigs / sum(eigs)

##  [1] 3.727273e-01 5.893710e-02 4.636826e-02 3.872259e-02 3.092701e-02
##  [6] 2.972575e-02 2.815171e-02 2.458349e-02 2.335775e-02 2.179461e-02
## [11] 2.094482e-02 1.983032e-02 1.971037e-02 1.890147e-02 1.815546e-02
## [16] 1.645922e-02 1.586850e-02 1.535524e-02 1.358035e-02 1.325778e-02
## [21] 1.237912e-02 1.139682e-02 1.054847e-02 1.043613e-02 9.853225e-03
## [26] 9.106677e-03 8.968893e-03 8.218947e-03 7.690762e-03 6.999454e-03
## [31] 6.708383e-03 6.052930e-03 5.779889e-03 5.646422e-03 4.946627e-03
## [36] 4.113569e-03 3.769103e-03 3.536379e-03 2.929205e-03 2.632044e-03
## [41] 2.324206e-03 2.239932e-03 1.606036e-03 1.453440e-03 1.174727e-03
## [46] 9.587481e-04 7.508943e-04 4.198617e-04 7.350751e-32

var.explained <- eigs / sum(eigs)
var.explained <- var.explained*100

#plot(pca$x[,1],pca$x[,2],cex=1.5, pch = 21, frame=F,lwd=1,cex.axis=1.4,cex.lab=1.4, bg = cols,
#     xlab=paste("\nPC1 (",round(as.numeric(var.explained[1]),1),"%)",sep=""),
#     ylab=paste("\nPC2 (",round(as.numeric(var.explained[2]),1),"%)",sep="")) + box(bty="l",lwd=3)

## PLSDA 
plsda.res <- splsda(otu_data, as.factor(meta_data$sample_type),ncomp = 3, max.iter = 2000)

#pdf("Kphyseq_sPLDA_sampletype.pdf",height=6,width=8,pointsize=15)  
plotIndiv(plsda.res, legend = T, title = "Sample type sPLSDA", ellipse = T, ind.names = T)

#dev.off()

########## Phylogeny profile############################# 
## phylogeny profile

## All dataset sample type at phylum level

phylogeny_profile(Kphyseq_norm_genus_prop_top, classification = 'Genus', 
                  treatment = "sample_type", merge = TRUE, 
                  relative_abundance = TRUE)

## Warning in conglomerate_taxa(phyloseq_obj, classification, hierarchical =
## FALSE): trees cannot be preserved after taxa conglomeration

####################
## taxa_abundance_bars

## All dataset sample type at phylum level

filtered_objA <- taxa_filter(Kphyseq, frequency = 0.8)
taxa_abundance_bars(filtered_objA, classification = 'Genus',
                    treatment = "sample_type")

#################

## Alpha diversity graph

## All dataset for sample type 

alpha_diversity_graph(Kphyseq_norm_genus_prop, index = 'shannon', treatment = "sample_type",
                      subset = NULL, colors = 'default')

alpha_diversity_graph(Kphyseq_norm_genus_prop_top, index = 'shannon', treatment = "sample_type",
                      subset = NULL, colors = 'default')

#############################################################################
#---------------------------------------------------------------------------------------------------
## PCOA phyloseq

## all dataset for sample type

pcoa_phyloseq(Kphyseq_norm_genus_prop_top, "sample_type", circle = TRUE)

pcoa_phyloseq(Kphyseq_norm_genus_prop, "sample_type", circle = TRUE)

#dev.off()
###########################################################################################################
###################################################################
##### Maternal diet Graphics
#pdf("Kphyseq_Maternal diet analysis.pdf",height=6,width=8,pointsize=15)  
## PCOA phyloseq

pcoa_phyloseq(Kphyseq_norm, "mdiet", circle = TRUE)

#################
## taxa_abundance_bars

## All dataset sample type at phylum level

filtered_objA <- taxa_filter(Kphyseq, frequency = 0.8)
taxa_abundance_bars(filtered_objA, classification = 'Genus',
                    treatment = "mdiet")

################################
##### Phylogeny profile

## All dataset sample type at genus level

phylogeny_profile(Kphyseq_norm_genus_prop_top, classification = 'Genus', 
                  treatment = "mdiet", merge = TRUE, 
                  relative_abundance = TRUE)

####################################################
## Alpha diversity graph

## All dataset for sample type 

alpha_diversity_graph(Kphyseq_norm, index = 'shannon', treatment = "mdiet",
                      subset = NULL, colors = 'default')

#############################
##Alpha diversity
##https://www.nicholas-ollberding.com/post/introduction-to-phyloseq/

head(estimate_richness(Kphyseq))

##     Observed    Chao1  se.chao1      ACE    se.ACE  Shannon   Simpson
## X10      467 467.0185 0.1416587 467.5622 10.798213 4.084574 0.9702991
## X11      396 396.0476 0.2288603 397.0564  9.942537 3.770247 0.9574684
## X12      413 413.0200 0.1476714 413.5525 10.151408 3.726533 0.9541814
## X13      665 665.0312 0.1824670 665.8932 12.862596 3.763168 0.9420338
## X14      398 398.0164 0.1326892 398.6201  9.968236 3.715440 0.9574987
## X23      548 548.0508 0.2372249 548.8994 11.700436 3.958817 0.9366669
##     InvSimpson   Fisher
## X10   33.66896 63.80074
## X11   23.51194 54.90173
## X12   21.82518 56.75878
## X13   17.25142 95.84068
## X14   23.52872 55.82140
## X23   15.78952 81.39638

(B <- plot_richness(Kphyseq, x = "mdiet", color = "mdiet", measures = c("Observed", "Shannon", "Chao1")))

B + labs(x = "", y = "Alpha Diversity Measure\n") + 
  geom_boxplot() 

######
## PCA

#pdf("Kphyseq_PCA_mdiet.pdf",height=6,width=8,pointsize=15)  
fviz_pca_ind(pca,
             habillage = meta_data$mdiet, # color by mdiet
             addEllipses = T, 
             ellipse.level=0.95,
             legend.title = "Maternal Diet",
             repel = F,
             pointsize = 3,
             label = "none",
             geom="point",
             invisible="quali",
             ggtheme = theme_bw())

#dev.off()

####
## PLSDA

plsda.resM <- splsda(otu_data, as.factor(meta_data$mdiet),ncomp = 3, max.iter = 2000)

#pdf("Kphyseq_sPLDA_sampletype.pdf",height=6,width=8,pointsize=15)  
plotIndiv(plsda.resM, legend = T, title = "Maternal diet sPLSDA", ellipse = T, ind.names = T)

#dev.off()

#dev.off()
#######################################################################################
################################################################################
#####################################
##Kitten diet 


## PCOA phyloseq

#pdf("Kphyseq_Kitten diet analysis.pdf",height=6,width=8,pointsize=15)  

pcoa_phyloseq(Kphyseq_norm, "kdiet", circle = TRUE)

#################
## taxa_abundance_bars

## All dataset sample type at phylum level

filtered_objA <- taxa_filter(Kphyseq, frequency = 0.8)

taxa_abundance_bars(filtered_objA, classification = 'Genus',
                    treatment = "kdiet")

################################
##### Phylogeny profile


phylogeny_profile(Kphyseq_norm_genus_prop_top, classification = 'Genus', 
                  treatment = "kdiet", merge = TRUE, 
                  relative_abundance = TRUE)

####################################################
## Alpha diversity graph

alpha_diversity_graph(Kphyseq, index = 'shannon', treatment = "kdiet",
                      subset = NULL, colors = 'default')

#############################
##Alpha diversity
##https://www.nicholas-ollberding.com/post/introduction-to-phyloseq/

head(estimate_richness(Kphyseq))

##     Observed    Chao1  se.chao1      ACE    se.ACE  Shannon   Simpson
## X10      467 467.0185 0.1416587 467.5622 10.798213 4.084574 0.9702991
## X11      396 396.0476 0.2288603 397.0564  9.942537 3.770247 0.9574684
## X12      413 413.0200 0.1476714 413.5525 10.151408 3.726533 0.9541814
## X13      665 665.0312 0.1824670 665.8932 12.862596 3.763168 0.9420338
## X14      398 398.0164 0.1326892 398.6201  9.968236 3.715440 0.9574987
## X23      548 548.0508 0.2372249 548.8994 11.700436 3.958817 0.9366669
##     InvSimpson   Fisher
## X10   33.66896 63.80074
## X11   23.51194 54.90173
## X12   21.82518 56.75878
## X13   17.25142 95.84068
## X14   23.52872 55.82140
## X23   15.78952 81.39638

(C <- plot_richness(Kphyseq, x = "kdiet", color = "kdiet", measures = c("Observed", "Shannon", "Chao1")))

C + labs(x = "", y = "Alpha Diversity Measure\n") + 
  geom_boxplot()

######
## PCA

#pdf("Kphyseq_PCA_mdiet.pdf",height=6,width=8,pointsize=15)  
fviz_pca_ind(pca,
             habillage = meta_data$kdiet, # color by kdiet
             addEllipses = T, 
             ellipse.level=0.95,
             legend.title = "Kitten Diet",
             repel = F,
             pointsize = 3,
             label = "none",
             geom="point",
             invisible="quali",
             ggtheme = theme_bw())

#dev.off()

####
## PLSDA

plsda.resK <- splsda(otu_data, as.factor(meta_data$kdiet),ncomp = 3, max.iter = 2000)

#pdf("Kphyseq_sPLDA_sampletype.pdf",height=6,width=8,pointsize=15)  
plotIndiv(plsda.resK, legend = T, title = "Kitten diet sPLSDA", ellipse = T, ind.names = T)

#dev.off()

#dev.off()

#####################################################################################
#######################################################################
###################################################
##PLSDA sample type and maternal diet
#pdf("Kphyseq_sample type diet PLSDA comparison.pdf",height=6,width=8,pointsize=15)  
plotIndiv(plsda.res, ind.names = FALSE,
          group = meta_data$sample_type,
          pch = as.factor(meta_data$mdiet) , 
          legend = TRUE, title = 'Sample type by maternal diet PLSDA',
          legend.title = 'Sample Type', 
          legend.title.pch = 'Maternal Diet', 
          point.lwd =1, star = FALSE, ellipse = T,)

##PLSDA sample type and kitten diet

plotIndiv(plsda.res, ind.names = FALSE,
          group = meta_data$sample_type,
          pch = as.factor(meta_data$kdiet) , 
          legend = TRUE, title = 'Sample type by Kitten diet PLSDA',
          legend.title = 'Sample Type', 
          legend.title.pch = 'Kitten Diet', 
          point.lwd =1, star = FALSE, ellipse = T,)

#dev.off()


############################################################################################
#pdf("Kphyseq_alpha diversity boxplot graph.pdf",height=6,width=8,pointsize=15)

par(mfrow=c(1,2))


## Alpha diversity graph

alpha_diversity_graph(Kphyseq, index = 'shannon', treatment = "sample_type",
                      subset = c("Pw-PD", "Pw-D", "W-R"), colors = 'default')

alpha_diversity_graph(Kphyseq, index = 'shannon', treatment = "sample_type",
                      subset = c("Pw-N", "W-N"), colors = 'default')

#dev.off()


#pdf("kphyseq_alpha diversity line graph.pdf",height=6,width=8,pointsize=15)

#par(mfrow=c(1,2))

###How to get the plot richness to work with the subsets of sample type??

#dev.off()



#--------------------------------------------------------------------------------
##PLSDA sample type and owner
#pdf("Kphyseq_sample type and owner PLSDA comparison.pdf",height=6,width=8,pointsize=15)  
plotIndiv(plsda.res, ind.names = FALSE,
          group = meta_data$sample_type,
          pch = as.factor(meta_data$owner) , 
          legend = TRUE, title = 'Sample type by owner PLSDA',
          legend.title = 'Sample Type', 
          legend.title.pch = 'owner', 
          point.lwd =1, star = FALSE, ellipse = T,)

##PLSDA sample type and owner

plotIndiv(plsda.res, ind.names = FALSE,
          group = meta_data$sample_type,
          pch = as.factor(meta_data$owner) , 
          legend = TRUE, title = 'Sample type by owner PLSDA',
          legend.title = 'Sample Type', 
          legend.title.pch = 'owner', 
          point.lwd =1, star = FALSE, ellipse = T,)

#dev.off()


######---------------------------------------------------------------------------------------

## PCOA phyloseq

#pdf("Kphyseq_owner analysis.pdf",height=6,width=8,pointsize=15)  

pcoa_phyloseq(Kphyseq_norm, "owner", circle = TRUE)

#dev.off()

#----------------------------------------------------------------------------------------------

taxa_proportions(Kphyseq_norm_genus, 'Genus', treatment = NULL)

##                   Genus Proportion
##                  <char>      <num>
##   1:        Bacteroides     0.2791
##   2:         Prevotella     0.2416
##   3:       [Prevotella]     0.1315
##   4:      Succinivibrio     0.0177
##   5: Anaerobiospirillum     0.0383
##  ---                              
## 375:         Roseomonas     0.0000
## 376:         Haloplasma     0.0000
## 377:        Helcococcus     0.0000
## 378:            R18-435     0.0000
## 379:          Marivirga     0.0000

view(taxa_proportions(Kphyseq_norm_genus, 'Genus', treatment = NULL))

#--------------------------------------------------------------------------------------------------------------------------------
###Run for kdiet, sample_type, owner, queenKitten
##### code found from = https://f1000research.com/articles/5-1492/v1 
top <- names(sort(taxa_sums(Kphyseq_norm_genus), decreasing = TRUE))[1:N]
N2 <- 20
top2 <- names(sort(taxa_sums(Kphyseq_norm_genus), decreasing = TRUE))[1:N2]

N3 <- 30
top3 <- names(sort(taxa_sums(Kphyseq_norm_genus), decreasing = TRUE))[1:N3]

Kphyseq_norm_genus_top <- prune_taxa(top3, Kphyseq_norm_genus)

plot_abundance = function(Kphyseq_norm_genus_top, ylabn = "",
                          Facet = "Genus",
                          Color = "Genus"){
  mKphyseq = psmelt(Kphyseq_norm_genus_top)
  mKphyseq <- subset(mKphyseq, Abundance > 0)
  ggplot(data = mKphyseq,
         mapping = aes_string(x = "sample_type", y = "Abundance",
                              color = Color, fill = Color)) +
    geom_violin(fill = NA) +
    geom_point(size = 1, alpha = 0.3,
               position = position_jitter(width = 0.3)) +
    facet_wrap(facets = Facet) + ylab(ylabn) +
    scale_y_log10()
}

KphyseqRA = transform_sample_counts(Kphyseq_norm_genus_top, function(x){x / sum(x)})
KphyseqRA1 = transform_sample_counts(Kphyseq_norm_genus, function(x){x / sum(x)})

#library("phyloseq")
#library("ggplot2")
#library("gridExtra")

plot_abundance(Kphyseq_norm_genus_top,"Original Abundances")

plot_abundance(KphyseqRA, "Relative Abundances")

#-----------------------------------------------------------------------------
#subset taxonomy
##Dysbiosis index indicator bacteria

view(Kphyseq@tax_table)

kphyseqDys1 = subset_taxa(KphyseqRA1, Genus == "Bacteroides") #Should be decreased if dysbiotic
kphyseqDys2 = subset_taxa(KphyseqRA1, Genus == "Bifidobacterium") #Should be decreased if dysbiotic
kphyseqDys3 = subset_taxa(KphyseqRA1, Genus == "Clostridium") #Should be decreased if dysbiotic. No C. Hiranonis
kphyseqDys4 = subset_taxa(KphyseqRA1, Genus == "Faecalibacterium") #Should be decreased if dysbiotic
#kphyseqDys5 = subset_taxa(KphyseqRA1, Genus == "Turicibacter") Not identified in this dataset
#kphyseqDys6 = subset_taxa(KphyseqRA1, Genus == "Enterobacteriaceae") #This is family of e.coli. Should be increased in pre-normal if dysbiotic
#p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae
kphyseqDys7 = subset_taxa(KphyseqRA1, Genus == "Streptococcus") #should be increased in pre-normal if dysbiotic
#Add Lachnospiraceae (family), genus Blautia not identified in this dataset


par(mfrow=c(2,2))
plot_abundance(kphyseqDys1, Facet = "Genus", Color = NULL)

plot_abundance(kphyseqDys2, Facet = "Genus", Color = NULL)

plot_abundance(kphyseqDys3, Facet = "Genus", Color = NULL)

plot_abundance(kphyseqDys4, Facet = "Genus", Color = NULL)

plot_abundance(kphyseqDys7, Facet = "Genus", Color = NULL)

#??subset_taxa

#-----------------------------------------------------------------------------------------------------------------------
# Top N taxa
N <- 10
topg1 <- names(sort(taxa_sums(Kphyseq_norm_genus), decreasing = TRUE))[1:N]

N2 <- 20
topg2 <- names(sort(taxa_sums(Kphyseq_norm_genus), decreasing = TRUE))[1:N2]

N3 <- 30
topg3 <- names(sort(taxa_sums(Kphyseq_norm_genus), decreasing = TRUE))[1:N3]
Kphyseq_norm_genus_prop <- transform_sample_counts(Kphyseq_norm_genus, function(x) x / sum(x) )

# Subset object to top N taxa
Kphyseq_norm_genus_prop_top <- prune_taxa(topg2, Kphyseq_norm_genus_prop)

Kphyseq_norm_genus_top <- prune_taxa(topg2, Kphyseq_norm_genus)

plot_abundance = function(Kphyseq_norm_genus_top, ylabn = "",
                          Facet = "Genus",
                          Color = "Genus"){
  mKphyseq = psmelt(Kphyseq_norm_genus_top)
  mKphyseq <- subset(mKphyseq, Abundance > 0)
  ggplot(data = mKphyseq,
         mapping = aes_string(x = "sample_type", y = "Abundance",
                              color = Color, fill = Color)) +
    geom_violin(fill = NA) +
    geom_point(size = 1, alpha = 0.3,
               position = position_jitter(width = 0.3)) +
    facet_wrap(facets = Facet) + ylab(ylabn) +
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
    scale_y_log10()
}

KphyseqRAg = transform_sample_counts(Kphyseq_norm_genus_top, function(x){x / sum(x)})
KphyseqRAg1 = transform_sample_counts(Kphyseq_norm_genus, function(x){x / sum(x)})

library("phyloseq")
library("ggplot2")
library("gridExtra")

## 
## Attaching package: 'gridExtra'
## 
## The following object is masked from 'package:dplyr':
## 
##     combine

plot_abundance(Kphyseq_norm_genus_top,"Original Abundances")

plot_abundance(KphyseqRAg, "Relative Abundances")